Starting phenix.real_space_refine on Tue Jun 25 10:44:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x19_37988/06_2024/8x19_37988_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x19_37988/06_2024/8x19_37988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x19_37988/06_2024/8x19_37988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x19_37988/06_2024/8x19_37988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x19_37988/06_2024/8x19_37988_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x19_37988/06_2024/8x19_37988_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 312 5.49 5 Mg 1 5.21 5 S 256 5.16 5 Be 1 3.05 5 C 34778 2.51 5 N 10076 2.21 5 O 11277 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 2032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 36": "NH1" <-> "NH2" Residue "K PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 317": "NH1" <-> "NH2" Residue "O PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 216": "OD1" <-> "OD2" Residue "R PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 120": "OE1" <-> "OE2" Residue "V PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 257": "NH1" <-> "NH2" Residue "W TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 171": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 56704 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "C" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 808 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "H" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "I" Number of atoms: 7122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 7122 Classifications: {'peptide': 864} Link IDs: {'PTRANS': 52, 'TRANS': 811} Chain breaks: 2 Chain: "J" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1350 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 13, 'TRANS': 148} Chain breaks: 1 Chain: "K" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3209 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain: "L" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain breaks: 1 Chain: "M" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3213 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3185 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 10, 'TRANS': 400} Chain breaks: 2 Chain: "O" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3287 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3368 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 422} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3293 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 10, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "T" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3146 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 1 Chain: "U" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2802 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Chain: "V" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1757 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain breaks: 1 Chain: "W" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1542 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 178} Chain: "X" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "Y" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2990 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.09, per 1000 atoms: 0.39 Number of scatterers: 56704 At special positions: 0 Unit cell: (184.092, 189.428, 225.446, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 256 16.00 P 312 15.00 Mg 1 11.99 F 3 9.00 O 11277 8.00 N 10076 7.00 C 34778 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.39 Conformation dependent library (CDL) restraints added in 6.6 seconds 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 269 helices and 43 sheets defined 43.4% alpha, 11.4% beta 124 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 19.22 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 removed outlier: 3.523A pdb=" N ALA A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 22' Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 48 through 74 removed outlier: 3.637A pdb=" N LEU A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 removed outlier: 4.871A pdb=" N LEU A 86 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 89 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.717A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'B' and resid 35 through 45 Processing helix chain 'B' and resid 53 through 80 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 101 through 116 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.625A pdb=" N LEU C 70 " --> pdb=" O PRO C 66 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 114 removed outlier: 3.678A pdb=" N ALA C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 31 through 40 removed outlier: 3.581A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 74 removed outlier: 4.164A pdb=" N GLU D 74 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'E' and resid 19 through 21 No H-bonds generated for 'chain 'E' and resid 19 through 21' Processing helix chain 'E' and resid 27 through 36 Processing helix chain 'E' and resid 47 through 72 Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 91 through 96 removed outlier: 3.649A pdb=" N LYS E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 45 removed outlier: 3.785A pdb=" N GLN F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 80 removed outlier: 3.545A pdb=" N GLU F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 96 Processing helix chain 'F' and resid 102 through 119 removed outlier: 3.545A pdb=" N SER F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 54 Processing helix chain 'G' and resid 64 through 77 removed outlier: 4.061A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 113 removed outlier: 3.807A pdb=" N MET G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 130 Processing helix chain 'H' and resid 26 through 28 No H-bonds generated for 'chain 'H' and resid 26 through 28' Processing helix chain 'H' and resid 31 through 40 Processing helix chain 'H' and resid 48 through 75 removed outlier: 3.911A pdb=" N TYR H 51 " --> pdb=" O GLY H 48 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU H 52 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU H 53 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR H 54 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG H 55 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU H 58 " --> pdb=" O ARG H 55 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS H 59 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL H 60 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU H 62 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU H 63 " --> pdb=" O VAL H 60 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE H 66 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG H 67 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP H 68 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL H 70 " --> pdb=" O ARG H 67 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU H 74 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS H 75 " --> pdb=" O TYR H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 93 Processing helix chain 'I' and resid 93 through 115 removed outlier: 3.637A pdb=" N GLN I 99 " --> pdb=" O ILE I 96 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR I 108 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 250 removed outlier: 3.639A pdb=" N ALA I 149 " --> pdb=" O GLN I 145 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU I 180 " --> pdb=" O GLN I 176 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL I 202 " --> pdb=" O MET I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 620 through 634 Processing helix chain 'I' and resid 649 through 663 Processing helix chain 'I' and resid 676 through 689 removed outlier: 4.660A pdb=" N LEU I 680 " --> pdb=" O SER I 677 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU I 683 " --> pdb=" O LEU I 680 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU I 685 " --> pdb=" O TRP I 682 " (cutoff:3.500A) Processing helix chain 'I' and resid 702 through 709 removed outlier: 3.655A pdb=" N LYS I 706 " --> pdb=" O GLN I 702 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG I 709 " --> pdb=" O ARG I 705 " (cutoff:3.500A) Processing helix chain 'I' and resid 726 through 729 No H-bonds generated for 'chain 'I' and resid 726 through 729' Processing helix chain 'I' and resid 733 through 736 No H-bonds generated for 'chain 'I' and resid 733 through 736' Processing helix chain 'I' and resid 748 through 751 Processing helix chain 'I' and resid 759 through 763 Processing helix chain 'I' and resid 784 through 792 removed outlier: 3.974A pdb=" N LEU I 788 " --> pdb=" O GLU I 784 " (cutoff:3.500A) Processing helix chain 'I' and resid 801 through 813 Proline residue: I 810 - end of helix Processing helix chain 'I' and resid 826 through 833 removed outlier: 3.639A pdb=" N LEU I 833 " --> pdb=" O LEU I 829 " (cutoff:3.500A) Processing helix chain 'I' and resid 863 through 874 removed outlier: 3.584A pdb=" N ALA I 874 " --> pdb=" O ASP I 870 " (cutoff:3.500A) Processing helix chain 'I' and resid 876 through 883 Processing helix chain 'I' and resid 888 through 902 Processing helix chain 'I' and resid 904 through 907 No H-bonds generated for 'chain 'I' and resid 904 through 907' Processing helix chain 'I' and resid 928 through 931 No H-bonds generated for 'chain 'I' and resid 928 through 931' Processing helix chain 'I' and resid 943 through 945 No H-bonds generated for 'chain 'I' and resid 943 through 945' Processing helix chain 'I' and resid 949 through 951 No H-bonds generated for 'chain 'I' and resid 949 through 951' Processing helix chain 'I' and resid 957 through 961 Processing helix chain 'I' and resid 963 through 967 Processing helix chain 'I' and resid 971 through 977 Processing helix chain 'I' and resid 1887 through 1912 removed outlier: 3.970A pdb=" N GLY I1912 " --> pdb=" O SER I1908 " (cutoff:3.500A) Processing helix chain 'I' and resid 1920 through 1926 Processing helix chain 'I' and resid 1946 through 1948 No H-bonds generated for 'chain 'I' and resid 1946 through 1948' Processing helix chain 'I' and resid 1953 through 1958 removed outlier: 3.979A pdb=" N ALA I1958 " --> pdb=" O ALA I1954 " (cutoff:3.500A) Processing helix chain 'I' and resid 1962 through 1976 removed outlier: 4.381A pdb=" N GLU I1971 " --> pdb=" O ASP I1967 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE I1972 " --> pdb=" O GLN I1968 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG I1975 " --> pdb=" O GLU I1971 " (cutoff:3.500A) Processing helix chain 'I' and resid 1997 through 2013 removed outlier: 3.903A pdb=" N ALA I2000 " --> pdb=" O PRO I1997 " (cutoff:3.500A) Proline residue: I2001 - end of helix removed outlier: 3.513A pdb=" N ALA I2011 " --> pdb=" O GLU I2008 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER I2012 " --> pdb=" O GLN I2009 " (cutoff:3.500A) Processing helix chain 'I' and resid 2015 through 2027 Proline residue: I2020 - end of helix removed outlier: 4.564A pdb=" N ARG I2023 " --> pdb=" O ARG I2019 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE I2024 " --> pdb=" O PRO I2020 " (cutoff:3.500A) Processing helix chain 'I' and resid 2043 through 2056 Processing helix chain 'I' and resid 2072 through 2081 removed outlier: 3.660A pdb=" N THR I2080 " --> pdb=" O GLU I2076 " (cutoff:3.500A) Processing helix chain 'I' and resid 2095 through 2106 Processing helix chain 'I' and resid 2142 through 2151 removed outlier: 3.655A pdb=" N ARG I2151 " --> pdb=" O GLN I2147 " (cutoff:3.500A) Processing helix chain 'I' and resid 2172 through 2191 Processing helix chain 'J' and resid 135 through 155 Processing helix chain 'J' and resid 171 through 192 removed outlier: 3.597A pdb=" N GLU J 175 " --> pdb=" O GLU J 171 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA J 176 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR J 190 " --> pdb=" O SER J 186 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU J 191 " --> pdb=" O LEU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 276 Processing helix chain 'J' and resid 313 through 329 Processing helix chain 'K' and resid 42 through 47 Processing helix chain 'K' and resid 69 through 79 Processing helix chain 'K' and resid 104 through 115 Processing helix chain 'K' and resid 127 through 138 Processing helix chain 'K' and resid 177 through 191 Processing helix chain 'K' and resid 200 through 207 Processing helix chain 'K' and resid 216 through 223 Processing helix chain 'K' and resid 252 through 254 No H-bonds generated for 'chain 'K' and resid 252 through 254' Processing helix chain 'K' and resid 273 through 282 Proline residue: K 278 - end of helix Processing helix chain 'K' and resid 294 through 302 Processing helix chain 'K' and resid 307 through 316 Proline residue: K 311 - end of helix Processing helix chain 'K' and resid 323 through 325 No H-bonds generated for 'chain 'K' and resid 323 through 325' Processing helix chain 'K' and resid 329 through 340 Processing helix chain 'K' and resid 358 through 368 Processing helix chain 'K' and resid 379 through 382 No H-bonds generated for 'chain 'K' and resid 379 through 382' Processing helix chain 'K' and resid 388 through 393 Processing helix chain 'L' and resid 22 through 36 Processing helix chain 'L' and resid 84 through 93 Processing helix chain 'L' and resid 102 through 104 No H-bonds generated for 'chain 'L' and resid 102 through 104' Processing helix chain 'L' and resid 138 through 147 Processing helix chain 'M' and resid 43 through 58 removed outlier: 3.802A pdb=" N GLU M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU M 55 " --> pdb=" O VAL M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 87 Processing helix chain 'M' and resid 98 through 101 Processing helix chain 'M' and resid 108 through 118 Processing helix chain 'M' and resid 174 through 182 removed outlier: 3.783A pdb=" N LEU M 180 " --> pdb=" O PHE M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 248 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 275 through 289 Processing helix chain 'M' and resid 304 through 306 No H-bonds generated for 'chain 'M' and resid 304 through 306' Processing helix chain 'M' and resid 309 through 318 Processing helix chain 'M' and resid 347 through 349 No H-bonds generated for 'chain 'M' and resid 347 through 349' Processing helix chain 'M' and resid 352 through 355 No H-bonds generated for 'chain 'M' and resid 352 through 355' Processing helix chain 'M' and resid 368 through 382 Processing helix chain 'M' and resid 388 through 400 Processing helix chain 'M' and resid 403 through 419 removed outlier: 3.870A pdb=" N LEU M 410 " --> pdb=" O SER M 406 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N THR M 411 " --> pdb=" O VAL M 407 " (cutoff:3.500A) Proline residue: M 412 - end of helix Processing helix chain 'M' and resid 427 through 436 removed outlier: 3.817A pdb=" N GLU M 432 " --> pdb=" O GLU M 428 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU M 435 " --> pdb=" O GLU M 431 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU M 436 " --> pdb=" O GLU M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 440 through 449 removed outlier: 4.453A pdb=" N ASP M 449 " --> pdb=" O LYS M 445 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 65 Processing helix chain 'N' and resid 83 through 94 Processing helix chain 'N' and resid 105 through 108 removed outlier: 3.664A pdb=" N ILE N 108 " --> pdb=" O GLY N 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 105 through 108' Processing helix chain 'N' and resid 115 through 125 Processing helix chain 'N' and resid 176 through 185 removed outlier: 3.881A pdb=" N LYS N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP N 185 " --> pdb=" O SER N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 252 Processing helix chain 'N' and resid 258 through 260 No H-bonds generated for 'chain 'N' and resid 258 through 260' Processing helix chain 'N' and resid 274 through 283 Processing helix chain 'N' and resid 301 through 303 No H-bonds generated for 'chain 'N' and resid 301 through 303' Processing helix chain 'N' and resid 306 through 317 removed outlier: 3.966A pdb=" N ARG N 314 " --> pdb=" O SER N 310 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU N 317 " --> pdb=" O ASN N 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 345 No H-bonds generated for 'chain 'N' and resid 343 through 345' Processing helix chain 'N' and resid 348 through 353 removed outlier: 4.327A pdb=" N ARG N 353 " --> pdb=" O ASP N 349 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 377 Processing helix chain 'N' and resid 384 through 396 Processing helix chain 'N' and resid 399 through 415 removed outlier: 4.282A pdb=" N THR N 407 " --> pdb=" O ILE N 403 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA N 408 " --> pdb=" O GLN N 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 423 through 432 Processing helix chain 'N' and resid 436 through 441 Processing helix chain 'O' and resid 43 through 57 Processing helix chain 'O' and resid 78 through 87 Processing helix chain 'O' and resid 98 through 101 Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.762A pdb=" N LEU O 112 " --> pdb=" O LYS O 108 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG O 117 " --> pdb=" O MET O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 183 Processing helix chain 'O' and resid 207 through 211 removed outlier: 4.159A pdb=" N THR O 211 " --> pdb=" O THR O 208 " (cutoff:3.500A) Processing helix chain 'O' and resid 240 through 248 Processing helix chain 'O' and resid 257 through 259 No H-bonds generated for 'chain 'O' and resid 257 through 259' Processing helix chain 'O' and resid 272 through 275 No H-bonds generated for 'chain 'O' and resid 272 through 275' Processing helix chain 'O' and resid 278 through 289 Processing helix chain 'O' and resid 304 through 306 No H-bonds generated for 'chain 'O' and resid 304 through 306' Processing helix chain 'O' and resid 309 through 319 removed outlier: 3.559A pdb=" N HIS O 316 " --> pdb=" O PHE O 312 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 347 through 349 No H-bonds generated for 'chain 'O' and resid 347 through 349' Processing helix chain 'O' and resid 352 through 357 removed outlier: 3.984A pdb=" N ARG O 357 " --> pdb=" O ASP O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 368 through 381 Processing helix chain 'O' and resid 388 through 400 Processing helix chain 'O' and resid 403 through 419 removed outlier: 4.103A pdb=" N LEU O 410 " --> pdb=" O SER O 406 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR O 411 " --> pdb=" O VAL O 407 " (cutoff:3.500A) Proline residue: O 412 - end of helix Processing helix chain 'O' and resid 427 through 436 Processing helix chain 'O' and resid 440 through 449 removed outlier: 4.342A pdb=" N LYS O 445 " --> pdb=" O LYS O 441 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE O 446 " --> pdb=" O SER O 442 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 453 No H-bonds generated for 'chain 'O' and resid 451 through 453' Processing helix chain 'P' and resid 43 through 45 No H-bonds generated for 'chain 'P' and resid 43 through 45' Processing helix chain 'P' and resid 50 through 65 Processing helix chain 'P' and resid 83 through 94 Processing helix chain 'P' and resid 105 through 108 removed outlier: 3.799A pdb=" N ILE P 108 " --> pdb=" O GLY P 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 105 through 108' Processing helix chain 'P' and resid 115 through 126 removed outlier: 3.802A pdb=" N SER P 126 " --> pdb=" O ALA P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 185 removed outlier: 3.543A pdb=" N ASP P 185 " --> pdb=" O SER P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 244 through 252 Processing helix chain 'P' and resid 257 through 261 Processing helix chain 'P' and resid 273 through 286 Processing helix chain 'P' and resid 301 through 303 No H-bonds generated for 'chain 'P' and resid 301 through 303' Processing helix chain 'P' and resid 306 through 315 removed outlier: 4.003A pdb=" N ARG P 314 " --> pdb=" O SER P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 345 No H-bonds generated for 'chain 'P' and resid 343 through 345' Processing helix chain 'P' and resid 351 through 353 No H-bonds generated for 'chain 'P' and resid 351 through 353' Processing helix chain 'P' and resid 364 through 377 Processing helix chain 'P' and resid 384 through 396 Processing helix chain 'P' and resid 399 through 416 removed outlier: 3.607A pdb=" N ILE P 406 " --> pdb=" O ALA P 402 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR P 407 " --> pdb=" O ILE P 403 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA P 408 " --> pdb=" O GLN P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 423 through 432 Processing helix chain 'P' and resid 437 through 442 Processing helix chain 'Q' and resid 36 through 38 No H-bonds generated for 'chain 'Q' and resid 36 through 38' Processing helix chain 'Q' and resid 43 through 57 removed outlier: 3.501A pdb=" N GLU Q 54 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 87 removed outlier: 3.846A pdb=" N ALA Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 118 Processing helix chain 'Q' and resid 174 through 183 Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 256 through 259 Processing helix chain 'Q' and resid 272 through 275 No H-bonds generated for 'chain 'Q' and resid 272 through 275' Processing helix chain 'Q' and resid 280 through 289 Processing helix chain 'Q' and resid 304 through 306 No H-bonds generated for 'chain 'Q' and resid 304 through 306' Processing helix chain 'Q' and resid 309 through 319 removed outlier: 3.522A pdb=" N HIS Q 316 " --> pdb=" O PHE Q 312 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG Q 317 " --> pdb=" O THR Q 313 " (cutoff:3.500A) Processing helix chain 'Q' and resid 347 through 349 No H-bonds generated for 'chain 'Q' and resid 347 through 349' Processing helix chain 'Q' and resid 352 through 357 removed outlier: 4.196A pdb=" N ARG Q 357 " --> pdb=" O ASP Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 382 Processing helix chain 'Q' and resid 388 through 400 removed outlier: 3.726A pdb=" N LYS Q 400 " --> pdb=" O GLU Q 396 " (cutoff:3.500A) Processing helix chain 'Q' and resid 403 through 419 removed outlier: 4.373A pdb=" N LEU Q 410 " --> pdb=" O SER Q 406 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N THR Q 411 " --> pdb=" O VAL Q 407 " (cutoff:3.500A) Proline residue: Q 412 - end of helix Processing helix chain 'Q' and resid 427 through 436 Processing helix chain 'Q' and resid 440 through 449 Processing helix chain 'R' and resid 50 through 65 Processing helix chain 'R' and resid 83 through 93 Processing helix chain 'R' and resid 105 through 108 removed outlier: 3.804A pdb=" N ILE R 108 " --> pdb=" O GLY R 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 105 through 108' Processing helix chain 'R' and resid 115 through 126 Processing helix chain 'R' and resid 176 through 183 Processing helix chain 'R' and resid 213 through 215 No H-bonds generated for 'chain 'R' and resid 213 through 215' Processing helix chain 'R' and resid 244 through 250 Processing helix chain 'R' and resid 256 through 259 Processing helix chain 'R' and resid 269 through 272 No H-bonds generated for 'chain 'R' and resid 269 through 272' Processing helix chain 'R' and resid 275 through 286 Processing helix chain 'R' and resid 301 through 303 No H-bonds generated for 'chain 'R' and resid 301 through 303' Processing helix chain 'R' and resid 306 through 316 removed outlier: 3.935A pdb=" N ARG R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 345 No H-bonds generated for 'chain 'R' and resid 343 through 345' Processing helix chain 'R' and resid 348 through 353 removed outlier: 4.264A pdb=" N ARG R 353 " --> pdb=" O ASP R 349 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 378 removed outlier: 4.015A pdb=" N LYS R 368 " --> pdb=" O GLU R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 394 Processing helix chain 'R' and resid 399 through 415 removed outlier: 3.636A pdb=" N ILE R 403 " --> pdb=" O LEU R 399 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN R 404 " --> pdb=" O ARG R 400 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE R 406 " --> pdb=" O ALA R 402 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR R 407 " --> pdb=" O ILE R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 423 through 430 removed outlier: 3.561A pdb=" N LYS R 427 " --> pdb=" O VAL R 423 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 441 Processing helix chain 'S' and resid 55 through 59 Processing helix chain 'S' and resid 79 through 91 Processing helix chain 'S' and resid 98 through 100 No H-bonds generated for 'chain 'S' and resid 98 through 100' Processing helix chain 'S' and resid 113 through 125 Processing helix chain 'S' and resid 137 through 144 Processing helix chain 'S' and resid 182 through 195 Processing helix chain 'S' and resid 203 through 216 removed outlier: 3.847A pdb=" N GLU S 207 " --> pdb=" O THR S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 223 through 232 Processing helix chain 'S' and resid 252 through 261 removed outlier: 3.670A pdb=" N ARG S 256 " --> pdb=" O GLU S 253 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N CYS S 257 " --> pdb=" O ARG S 254 " (cutoff:3.500A) Proline residue: S 258 - end of helix Processing helix chain 'S' and resid 264 through 267 Processing helix chain 'S' and resid 274 through 284 Processing helix chain 'S' and resid 287 through 296 removed outlier: 4.325A pdb=" N LYS S 291 " --> pdb=" O VAL S 287 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASP S 292 " --> pdb=" O ASP S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 302 through 304 No H-bonds generated for 'chain 'S' and resid 302 through 304' Processing helix chain 'S' and resid 309 through 320 Processing helix chain 'S' and resid 338 through 348 removed outlier: 3.722A pdb=" N GLY S 343 " --> pdb=" O VAL S 339 " (cutoff:3.500A) Processing helix chain 'S' and resid 351 through 354 removed outlier: 3.726A pdb=" N GLN S 354 " --> pdb=" O THR S 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 351 through 354' Processing helix chain 'S' and resid 359 through 365 Processing helix chain 'S' and resid 367 through 373 Processing helix chain 'T' and resid 96 through 109 Processing helix chain 'T' and resid 115 through 117 No H-bonds generated for 'chain 'T' and resid 115 through 117' Processing helix chain 'T' and resid 130 through 143 Processing helix chain 'T' and resid 154 through 161 Processing helix chain 'T' and resid 189 through 191 No H-bonds generated for 'chain 'T' and resid 189 through 191' Processing helix chain 'T' and resid 199 through 212 Processing helix chain 'T' and resid 220 through 222 No H-bonds generated for 'chain 'T' and resid 220 through 222' Processing helix chain 'T' and resid 248 through 265 Processing helix chain 'T' and resid 276 through 281 Processing helix chain 'T' and resid 299 through 309 Proline residue: T 305 - end of helix removed outlier: 4.367A pdb=" N LEU T 308 " --> pdb=" O ILE T 304 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE T 309 " --> pdb=" O PRO T 305 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 313 No H-bonds generated for 'chain 'T' and resid 311 through 313' Processing helix chain 'T' and resid 325 through 334 Processing helix chain 'T' and resid 338 through 347 Proline residue: T 342 - end of helix Processing helix chain 'T' and resid 353 through 356 Processing helix chain 'T' and resid 360 through 371 Processing helix chain 'T' and resid 386 through 402 removed outlier: 6.415A pdb=" N SER T 393 " --> pdb=" O ARG T 389 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TRP T 394 " --> pdb=" O ARG T 390 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER T 402 " --> pdb=" O SER T 398 " (cutoff:3.500A) Processing helix chain 'T' and resid 404 through 406 No H-bonds generated for 'chain 'T' and resid 404 through 406' Processing helix chain 'T' and resid 413 through 419 Processing helix chain 'T' and resid 421 through 426 removed outlier: 3.913A pdb=" N VAL T 424 " --> pdb=" O LYS T 421 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 63 removed outlier: 6.234A pdb=" N GLY U 63 " --> pdb=" O GLN U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 92 removed outlier: 3.810A pdb=" N TYR U 91 " --> pdb=" O HIS U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 125 removed outlier: 3.977A pdb=" N GLU U 117 " --> pdb=" O LYS U 113 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS U 118 " --> pdb=" O ALA U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 137 through 145 removed outlier: 3.797A pdb=" N TYR U 143 " --> pdb=" O VAL U 139 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA U 144 " --> pdb=" O LEU U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 192 Processing helix chain 'U' and resid 203 through 214 removed outlier: 4.161A pdb=" N ILE U 208 " --> pdb=" O ALA U 204 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP U 211 " --> pdb=" O GLU U 207 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS U 213 " --> pdb=" O VAL U 209 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLU U 214 " --> pdb=" O ARG U 210 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 230 removed outlier: 3.639A pdb=" N ALA U 230 " --> pdb=" O GLU U 226 " (cutoff:3.500A) Processing helix chain 'U' and resid 252 through 254 No H-bonds generated for 'chain 'U' and resid 252 through 254' Processing helix chain 'U' and resid 258 through 261 Processing helix chain 'U' and resid 264 through 267 No H-bonds generated for 'chain 'U' and resid 264 through 267' Processing helix chain 'U' and resid 274 through 284 Processing helix chain 'U' and resid 289 through 295 removed outlier: 3.654A pdb=" N TYR U 294 " --> pdb=" O LYS U 291 " (cutoff:3.500A) Processing helix chain 'U' and resid 302 through 305 Processing helix chain 'U' and resid 308 through 318 removed outlier: 4.474A pdb=" N ILE U 317 " --> pdb=" O MET U 313 " (cutoff:3.500A) Processing helix chain 'U' and resid 335 through 347 removed outlier: 3.679A pdb=" N SER U 338 " --> pdb=" O ARG U 335 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL U 339 " --> pdb=" O LYS U 336 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE U 341 " --> pdb=" O SER U 338 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY U 343 " --> pdb=" O TRP U 340 " (cutoff:3.500A) Processing helix chain 'U' and resid 353 through 355 No H-bonds generated for 'chain 'U' and resid 353 through 355' Processing helix chain 'U' and resid 359 through 365 Processing helix chain 'V' and resid 55 through 62 Processing helix chain 'V' and resid 140 through 146 Processing helix chain 'V' and resid 154 through 166 removed outlier: 3.920A pdb=" N HIS V 159 " --> pdb=" O ALA V 155 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU V 160 " --> pdb=" O GLU V 156 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE V 161 " --> pdb=" O THR V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 171 through 174 No H-bonds generated for 'chain 'V' and resid 171 through 174' Processing helix chain 'V' and resid 188 through 206 removed outlier: 3.649A pdb=" N ARG V 206 " --> pdb=" O LEU V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 221 through 234 removed outlier: 3.759A pdb=" N LEU V 230 " --> pdb=" O ARG V 226 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU V 231 " --> pdb=" O LYS V 227 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU V 233 " --> pdb=" O GLN V 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 254 removed outlier: 3.945A pdb=" N ILE V 254 " --> pdb=" O LEU V 251 " (cutoff:3.500A) Processing helix chain 'V' and resid 262 through 274 Processing helix chain 'W' and resid 59 through 61 No H-bonds generated for 'chain 'W' and resid 59 through 61' Processing helix chain 'W' and resid 124 through 128 Processing helix chain 'W' and resid 149 through 156 Processing helix chain 'W' and resid 172 through 203 removed outlier: 3.779A pdb=" N LYS W 182 " --> pdb=" O LYS W 178 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA W 185 " --> pdb=" O GLU W 181 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'I' and resid 639 through 641 removed outlier: 6.209A pdb=" N LEU I 671 " --> pdb=" O ILE I 744 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER I 724 " --> pdb=" O TYR I 698 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 852 through 859 removed outlier: 6.825A pdb=" N VAL I2161 " --> pdb=" O TYR I 853 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N HIS I 855 " --> pdb=" O VAL I2161 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE I2163 " --> pdb=" O HIS I 855 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE I 857 " --> pdb=" O ILE I2163 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ARG I2165 " --> pdb=" O ILE I 857 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS I 859 " --> pdb=" O ARG I2165 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE I2167 " --> pdb=" O CYS I 859 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL I2133 " --> pdb=" O TYR I2164 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU I2166 " --> pdb=" O VAL I2133 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N PHE I2135 " --> pdb=" O LEU I2166 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N SER I2168 " --> pdb=" O PHE I2135 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'I' and resid 923 through 925 removed outlier: 6.191A pdb=" N LEU I1990 " --> pdb=" O SER I 924 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'I' and resid 2062 through 2065 Processing sheet with id= E, first strand: chain 'J' and resid 213 through 217 Processing sheet with id= F, first strand: chain 'K' and resid 54 through 58 Processing sheet with id= G, first strand: chain 'K' and resid 146 through 149 Processing sheet with id= H, first strand: chain 'M' and resid 359 through 362 removed outlier: 6.504A pdb=" N VAL M 327 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU M 68 " --> pdb=" O VAL M 327 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE M 329 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 292 through 296 Processing sheet with id= J, first strand: chain 'M' and resid 229 through 234 removed outlier: 6.934A pdb=" N TYR M 192 " --> pdb=" O ARG M 202 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG M 202 " --> pdb=" O TYR M 192 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'M' and resid 166 through 173 removed outlier: 3.882A pdb=" N HIS M 156 " --> pdb=" O CYS M 141 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU M 137 " --> pdb=" O GLY M 160 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS M 162 " --> pdb=" O VAL M 135 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL M 135 " --> pdb=" O LYS M 162 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 355 through 358 removed outlier: 6.643A pdb=" N LEU N 324 " --> pdb=" O VAL N 73 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE N 75 " --> pdb=" O LEU N 324 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET N 326 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 289 through 293 Processing sheet with id= N, first strand: chain 'N' and resid 168 through 174 removed outlier: 3.712A pdb=" N GLY N 159 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU N 144 " --> pdb=" O THR N 162 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS N 164 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL N 142 " --> pdb=" O LYS N 164 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP N 191 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY N 206 " --> pdb=" O VAL N 192 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR N 194 " --> pdb=" O LYS N 204 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS N 204 " --> pdb=" O THR N 194 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP N 196 " --> pdb=" O ILE N 202 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE N 202 " --> pdb=" O ASP N 196 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'N' and resid 332 through 334 Processing sheet with id= P, first strand: chain 'O' and resid 359 through 362 removed outlier: 6.573A pdb=" N VAL O 327 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU O 68 " --> pdb=" O VAL O 327 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE O 329 " --> pdb=" O LEU O 68 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'O' and resid 292 through 296 removed outlier: 3.814A pdb=" N LYS O 128 " --> pdb=" O LYS O 232 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS O 232 " --> pdb=" O LYS O 128 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'O' and resid 166 through 172 removed outlier: 3.746A pdb=" N HIS O 156 " --> pdb=" O CYS O 141 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU O 137 " --> pdb=" O GLY O 160 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS O 162 " --> pdb=" O VAL O 135 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL O 135 " --> pdb=" O LYS O 162 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP O 189 " --> pdb=" O VAL O 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY O 204 " --> pdb=" O VAL O 190 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR O 192 " --> pdb=" O ARG O 202 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARG O 202 " --> pdb=" O TYR O 192 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLU O 194 " --> pdb=" O VAL O 200 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL O 200 " --> pdb=" O GLU O 194 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'O' and resid 335 through 337 Processing sheet with id= T, first strand: chain 'P' and resid 354 through 359 removed outlier: 6.754A pdb=" N ALA P 72 " --> pdb=" O LEU P 355 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL P 357 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU P 74 " --> pdb=" O VAL P 357 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR P 359 " --> pdb=" O LEU P 74 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA P 76 " --> pdb=" O THR P 359 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU P 324 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE P 75 " --> pdb=" O LEU P 324 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N MET P 326 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLY P 77 " --> pdb=" O MET P 326 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR P 328 " --> pdb=" O GLY P 77 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 289 through 293 Processing sheet with id= V, first strand: chain 'P' and resid 168 through 174 removed outlier: 4.139A pdb=" N GLY P 159 " --> pdb=" O LEU P 174 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS P 164 " --> pdb=" O VAL P 142 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL P 142 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP P 191 " --> pdb=" O VAL P 142 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY P 206 " --> pdb=" O VAL P 192 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR P 194 " --> pdb=" O LYS P 204 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS P 204 " --> pdb=" O THR P 194 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASP P 196 " --> pdb=" O ILE P 202 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE P 202 " --> pdb=" O ASP P 196 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 359 through 362 removed outlier: 6.490A pdb=" N VAL Q 327 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU Q 68 " --> pdb=" O VAL Q 327 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE Q 329 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 292 through 296 Processing sheet with id= Y, first strand: chain 'Q' and resid 167 through 172 removed outlier: 3.745A pdb=" N HIS Q 156 " --> pdb=" O CYS Q 141 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU Q 137 " --> pdb=" O GLY Q 160 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS Q 162 " --> pdb=" O VAL Q 135 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL Q 135 " --> pdb=" O LYS Q 162 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY Q 133 " --> pdb=" O ILE Q 191 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE Q 191 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP Q 189 " --> pdb=" O VAL Q 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR Q 192 " --> pdb=" O ARG Q 202 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ARG Q 202 " --> pdb=" O TYR Q 192 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLU Q 194 " --> pdb=" O VAL Q 200 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL Q 200 " --> pdb=" O GLU Q 194 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'R' and resid 355 through 359 removed outlier: 6.481A pdb=" N LEU R 324 " --> pdb=" O VAL R 73 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE R 75 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N MET R 326 " --> pdb=" O ILE R 75 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLY R 77 " --> pdb=" O MET R 326 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR R 328 " --> pdb=" O GLY R 77 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'R' and resid 291 through 293 Processing sheet with id= AB, first strand: chain 'R' and resid 168 through 174 removed outlier: 3.978A pdb=" N GLY R 159 " --> pdb=" O LEU R 174 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU R 144 " --> pdb=" O THR R 162 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS R 164 " --> pdb=" O VAL R 142 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL R 142 " --> pdb=" O LYS R 164 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP R 191 " --> pdb=" O VAL R 142 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR R 194 " --> pdb=" O SER R 203 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER R 203 " --> pdb=" O THR R 194 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'R' and resid 332 through 334 Processing sheet with id= AD, first strand: chain 'S' and resid 132 through 136 removed outlier: 6.602A pdb=" N VAL S 103 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ALA S 135 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU S 105 " --> pdb=" O ALA S 135 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU S 8 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR S 106 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL S 10 " --> pdb=" O THR S 106 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'S' and resid 35 through 38 Processing sheet with id= AF, first strand: chain 'S' and resid 297 through 300 removed outlier: 6.443A pdb=" N ILE S 151 " --> pdb=" O VAL S 298 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER S 300 " --> pdb=" O ILE S 151 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N MET S 153 " --> pdb=" O SER S 300 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'S' and resid 238 through 241 Processing sheet with id= AH, first strand: chain 'T' and resid 35 through 38 removed outlier: 7.664A pdb=" N PHE T 16 " --> pdb=" O PRO T 119 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU T 121 " --> pdb=" O PHE T 16 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE T 18 " --> pdb=" O LEU T 121 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER T 123 " --> pdb=" O ILE T 18 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'T' and resid 42 through 44 Processing sheet with id= AJ, first strand: chain 'T' and resid 349 through 351 Processing sheet with id= AK, first strand: chain 'T' and resid 285 through 288 Processing sheet with id= AL, first strand: chain 'T' and resid 223 through 227 removed outlier: 6.774A pdb=" N LYS T 238 " --> pdb=" O ALA T 224 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS T 226 " --> pdb=" O ASN T 236 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN T 236 " --> pdb=" O LYS T 226 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'U' and resid 35 through 38 Processing sheet with id= AN, first strand: chain 'U' and resid 102 through 104 removed outlier: 6.362A pdb=" N ALA U 131 " --> pdb=" O VAL U 103 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'V' and resid 96 through 101 Processing sheet with id= AP, first strand: chain 'W' and resid 134 through 145 Processing sheet with id= AQ, first strand: chain 'W' and resid 78 through 81 removed outlier: 7.051A pdb=" N PHE W 103 " --> pdb=" O LYS W 64 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE W 66 " --> pdb=" O LYS W 101 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS W 101 " --> pdb=" O ILE W 66 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE W 68 " --> pdb=" O ILE W 99 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE W 99 " --> pdb=" O PHE W 68 " (cutoff:3.500A) 1967 hydrogen bonds defined for protein. 5430 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 319 hydrogen bonds 634 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 27.27 Time building geometry restraints manager: 20.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8897 1.31 - 1.44: 16115 1.44 - 1.56: 32274 1.56 - 1.69: 622 1.69 - 1.82: 426 Bond restraints: 58334 Sorted by residual: bond pdb=" C ASP L 12 " pdb=" O ASP L 12 " ideal model delta sigma weight residual 1.234 1.187 0.048 5.00e-03 4.00e+04 9.11e+01 bond pdb=" C LEU I 124 " pdb=" O LEU I 124 " ideal model delta sigma weight residual 1.234 1.203 0.032 5.00e-03 4.00e+04 4.00e+01 bond pdb=" C ARG J 165 " pdb=" O ARG J 165 " ideal model delta sigma weight residual 1.238 1.313 -0.075 1.28e-02 6.10e+03 3.45e+01 bond pdb=" CD1 PHE V 183 " pdb=" CE1 PHE V 183 " ideal model delta sigma weight residual 1.382 1.551 -0.169 3.00e-02 1.11e+03 3.19e+01 bond pdb=" CA ARG V 261 " pdb=" C ARG V 261 " ideal model delta sigma weight residual 1.524 1.564 -0.039 7.00e-03 2.04e+04 3.15e+01 ... (remaining 58329 not shown) Histogram of bond angle deviations from ideal: 92.84 - 102.26: 522 102.26 - 111.67: 28339 111.67 - 121.09: 34501 121.09 - 130.50: 16415 130.50 - 139.92: 284 Bond angle restraints: 80061 Sorted by residual: angle pdb=" N PRO I1995 " pdb=" CA PRO I1995 " pdb=" C PRO I1995 " ideal model delta sigma weight residual 110.70 122.49 -11.79 1.22e+00 6.72e-01 9.34e+01 angle pdb=" N TYR R 215 " pdb=" CA TYR R 215 " pdb=" C TYR R 215 " ideal model delta sigma weight residual 111.71 100.60 11.11 1.15e+00 7.56e-01 9.34e+01 angle pdb=" CB GLU V 156 " pdb=" CG GLU V 156 " pdb=" CD GLU V 156 " ideal model delta sigma weight residual 112.60 127.33 -14.73 1.70e+00 3.46e-01 7.51e+01 angle pdb=" N ARG M 317 " pdb=" CA ARG M 317 " pdb=" C ARG M 317 " ideal model delta sigma weight residual 113.50 103.75 9.75 1.23e+00 6.61e-01 6.28e+01 angle pdb=" C GLU V 260 " pdb=" N ARG V 261 " pdb=" CA ARG V 261 " ideal model delta sigma weight residual 122.44 114.43 8.01 1.19e+00 7.06e-01 4.54e+01 ... (remaining 80056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.78: 31870 31.78 - 63.55: 2809 63.55 - 95.33: 175 95.33 - 127.11: 7 127.11 - 158.89: 3 Dihedral angle restraints: 34864 sinusoidal: 16418 harmonic: 18446 Sorted by residual: dihedral pdb=" CA THR W 170 " pdb=" C THR W 170 " pdb=" N GLU W 171 " pdb=" CA GLU W 171 " ideal model delta harmonic sigma weight residual -180.00 -62.82 -117.18 0 5.00e+00 4.00e-02 5.49e+02 dihedral pdb=" CD ARG G 134 " pdb=" NE ARG G 134 " pdb=" CZ ARG G 134 " pdb=" NH1 ARG G 134 " ideal model delta sinusoidal sigma weight residual 0.00 72.94 -72.94 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CD ARG V 257 " pdb=" NE ARG V 257 " pdb=" CZ ARG V 257 " pdb=" NH1 ARG V 257 " ideal model delta sinusoidal sigma weight residual 0.00 71.34 -71.34 1 1.00e+01 1.00e-02 6.53e+01 ... (remaining 34861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 7785 0.065 - 0.129: 1081 0.129 - 0.194: 134 0.194 - 0.258: 10 0.258 - 0.323: 8 Chirality restraints: 9018 Sorted by residual: chirality pdb=" CG LEU K 89 " pdb=" CB LEU K 89 " pdb=" CD1 LEU K 89 " pdb=" CD2 LEU K 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' ATP T 501 " pdb=" C2' ATP T 501 " pdb=" C4' ATP T 501 " pdb=" O3' ATP T 501 " both_signs ideal model delta sigma weight residual False -2.63 -2.95 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C3' ATP U 401 " pdb=" C2' ATP U 401 " pdb=" C4' ATP U 401 " pdb=" O3' ATP U 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.94 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 9015 not shown) Planarity restraints: 9229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 134 " -1.054 9.50e-02 1.11e+02 4.73e-01 1.35e+02 pdb=" NE ARG G 134 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG G 134 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 134 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG G 134 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG V 257 " 1.031 9.50e-02 1.11e+02 4.62e-01 1.29e+02 pdb=" NE ARG V 257 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG V 257 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG V 257 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG V 257 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 18 " 0.589 9.50e-02 1.11e+02 2.64e-01 4.26e+01 pdb=" NE ARG P 18 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG P 18 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG P 18 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG P 18 " 0.018 2.00e-02 2.50e+03 ... (remaining 9226 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 52 2.18 - 2.86: 20525 2.86 - 3.54: 83269 3.54 - 4.22: 145707 4.22 - 4.90: 236066 Nonbonded interactions: 485619 Sorted by model distance: nonbonded pdb=" CD2 LEU I2014 " pdb=" CD1 ILE Q 256 " model vdw 1.500 3.880 nonbonded pdb=" CE2 TYR I 633 " pdb=" OH TYR I 742 " model vdw 1.503 3.340 nonbonded pdb=" OE2 GLU O 126 " pdb=" CE LYS O 128 " model vdw 1.512 3.440 nonbonded pdb=" OE2 GLU A 62 " pdb=" OE1 GLN L 15 " model vdw 1.586 3.040 nonbonded pdb=" CD GLU A 62 " pdb=" OE1 GLN L 15 " model vdw 1.627 3.270 ... (remaining 485614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 119) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 28 through 121) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 41 through 134) selection = (chain 'G' and resid 41 through 134) } ncs_group { reference = (chain 'D' and resid 23 through 102) selection = chain 'H' } ncs_group { reference = (chain 'M' and (resid 15 through 451 or resid 501)) selection = (chain 'O' and (resid 15 through 141 or resid 153 through 209 or resid 220 throu \ gh 451 or resid 501)) selection = (chain 'Q' and (resid 15 through 141 or resid 153 through 209 or resid 220 throu \ gh 451 or resid 501)) } ncs_group { reference = (chain 'N' and (resid 18 through 148 or resid 157 through 447 or resid 501)) selection = (chain 'P' and (resid 18 through 148 or resid 157 through 208 or resid 225 throu \ gh 447 or resid 501)) selection = (chain 'R' and (resid 18 through 208 or resid 225 through 447 or resid 501)) } ncs_group { reference = (chain 'S' and (resid 2 through 40 or resid 52 through 371)) selection = (chain 'U' and resid 2 through 371) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 13.560 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 132.650 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 58334 Z= 0.298 Angle : 0.834 14.730 80061 Z= 0.479 Chirality : 0.046 0.323 9018 Planarity : 0.011 0.473 9229 Dihedral : 20.515 158.885 22956 Min Nonbonded Distance : 1.500 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.59 % Favored : 92.93 % Rotamer: Outliers : 7.61 % Allowed : 8.91 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.10), residues: 6298 helix: -1.13 (0.09), residues: 2913 sheet: -0.46 (0.19), residues: 685 loop : -1.71 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 68 HIS 0.011 0.001 HIS M 316 PHE 0.054 0.002 PHE V 183 TYR 0.024 0.002 TYR K 64 ARG 0.013 0.001 ARG V 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 1240 time to evaluate : 4.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4739 (OUTLIER) cc_final: 0.4237 (mt) REVERT: B 28 ARG cc_start: 0.1816 (OUTLIER) cc_final: 0.1479 (mtp-110) REVERT: B 98 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6332 (mm) REVERT: E 73 ASN cc_start: 0.6531 (t160) cc_final: 0.6270 (t0) REVERT: F 28 ARG cc_start: 0.1037 (OUTLIER) cc_final: 0.0027 (mmt180) REVERT: I 825 LEU cc_start: 0.5794 (mp) cc_final: 0.5575 (mt) REVERT: I 2036 ARG cc_start: 0.7172 (mmm160) cc_final: 0.6321 (mtm110) REVERT: I 2073 ASP cc_start: 0.6724 (t0) cc_final: 0.6471 (m-30) REVERT: I 2109 LYS cc_start: 0.7565 (tppp) cc_final: 0.7228 (mppt) REVERT: J 174 ARG cc_start: 0.5065 (ttm-80) cc_final: 0.4827 (tmm-80) REVERT: K 34 THR cc_start: 0.3636 (OUTLIER) cc_final: 0.3428 (p) REVERT: K 38 LYS cc_start: 0.3265 (OUTLIER) cc_final: 0.3004 (mtpp) REVERT: K 69 ASP cc_start: 0.6392 (OUTLIER) cc_final: 0.6050 (p0) REVERT: K 106 GLN cc_start: 0.6749 (mt0) cc_final: 0.6282 (mt0) REVERT: K 109 MET cc_start: 0.6252 (ttm) cc_final: 0.5917 (ttp) REVERT: K 138 ASP cc_start: 0.5721 (OUTLIER) cc_final: 0.5173 (p0) REVERT: K 185 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.6917 (ttpp) REVERT: K 186 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6400 (tp30) REVERT: K 274 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.5580 (ptm160) REVERT: K 289 ILE cc_start: 0.6018 (OUTLIER) cc_final: 0.5795 (pt) REVERT: K 310 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6711 (mt0) REVERT: K 319 LEU cc_start: 0.6913 (mt) cc_final: 0.6671 (mp) REVERT: K 326 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.6080 (m-80) REVERT: K 383 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6074 (mt-10) REVERT: M 96 MET cc_start: 0.7535 (ttp) cc_final: 0.7282 (ttm) REVERT: M 306 MET cc_start: 0.7950 (mmm) cc_final: 0.7748 (mmp) REVERT: M 323 ILE cc_start: 0.8448 (pt) cc_final: 0.7915 (mt) REVERT: M 346 SER cc_start: 0.8911 (m) cc_final: 0.8300 (t) REVERT: N 267 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8135 (mp0) REVERT: N 381 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7269 (mp0) REVERT: N 436 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7305 (tm-30) REVERT: O 37 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.8034 (p) REVERT: O 259 MET cc_start: 0.7933 (mmm) cc_final: 0.7670 (tpt) REVERT: O 269 THR cc_start: 0.6820 (p) cc_final: 0.5837 (p) REVERT: O 270 GLU cc_start: 0.7230 (pt0) cc_final: 0.6980 (pp20) REVERT: O 271 ILE cc_start: 0.6472 (tt) cc_final: 0.6240 (tp) REVERT: O 323 ILE cc_start: 0.7839 (pt) cc_final: 0.7358 (mt) REVERT: O 392 ASN cc_start: 0.7582 (t0) cc_final: 0.7080 (m-40) REVERT: P 113 MET cc_start: 0.8142 (ptt) cc_final: 0.7756 (ptp) REVERT: P 117 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6419 (tp30) REVERT: P 168 MET cc_start: 0.7848 (ptm) cc_final: 0.6697 (ptp) REVERT: P 188 GLN cc_start: 0.8018 (pt0) cc_final: 0.7770 (pm20) REVERT: P 236 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8101 (pttm) REVERT: P 257 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.4753 (m-10) REVERT: P 261 PHE cc_start: 0.7122 (t80) cc_final: 0.6792 (t80) REVERT: P 267 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6857 (mm-30) REVERT: P 284 ARG cc_start: 0.6797 (ttt90) cc_final: 0.6541 (ttp-110) REVERT: Q 61 MET cc_start: 0.8283 (mmm) cc_final: 0.7976 (mmm) REVERT: Q 159 ILE cc_start: 0.7952 (tt) cc_final: 0.7674 (mt) REVERT: Q 165 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7150 (tptp) REVERT: Q 181 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7682 (tp-100) REVERT: Q 271 ILE cc_start: 0.7218 (mm) cc_final: 0.6971 (tt) REVERT: Q 308 ASP cc_start: 0.6696 (OUTLIER) cc_final: 0.6349 (t70) REVERT: R 67 LYS cc_start: 0.8003 (mttt) cc_final: 0.7519 (mmtt) REVERT: R 88 MET cc_start: 0.8179 (mmm) cc_final: 0.7794 (mmm) REVERT: R 145 ILE cc_start: 0.8332 (mt) cc_final: 0.8057 (mt) REVERT: R 225 VAL cc_start: 0.7082 (OUTLIER) cc_final: 0.6851 (m) REVERT: R 246 GLU cc_start: 0.4324 (OUTLIER) cc_final: 0.2864 (pt0) REVERT: R 374 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5812 (mmp-170) REVERT: R 387 TYR cc_start: 0.6956 (m-80) cc_final: 0.6655 (m-80) REVERT: S 44 MET cc_start: 0.0289 (mtp) cc_final: -0.0563 (tpp) REVERT: S 229 THR cc_start: 0.2688 (m) cc_final: 0.2339 (p) REVERT: S 296 ASN cc_start: 0.2884 (m-40) cc_final: 0.2342 (m-40) REVERT: T 303 LYS cc_start: 0.3733 (ttmt) cc_final: 0.3522 (ptpt) REVERT: U 24 ASP cc_start: 0.2822 (p0) cc_final: 0.2434 (p0) REVERT: U 227 MET cc_start: 0.0538 (mmt) cc_final: -0.1197 (ttp) REVERT: U 330 ILE cc_start: 0.0557 (OUTLIER) cc_final: -0.0141 (tt) REVERT: V 91 LYS cc_start: -0.0129 (OUTLIER) cc_final: -0.2210 (mtmm) REVERT: V 98 MET cc_start: -0.1640 (mtt) cc_final: -0.2624 (ppp) REVERT: V 111 PHE cc_start: -0.1785 (m-80) cc_final: -0.1991 (m-80) REVERT: V 120 GLU cc_start: 0.1759 (OUTLIER) cc_final: -0.0333 (mt-10) REVERT: V 134 GLN cc_start: 0.0108 (OUTLIER) cc_final: -0.0512 (pp30) REVERT: V 202 LEU cc_start: 0.2127 (OUTLIER) cc_final: 0.1669 (tp) REVERT: V 206 ARG cc_start: -0.0794 (OUTLIER) cc_final: -0.1372 (mpt180) REVERT: V 217 VAL cc_start: -0.0825 (OUTLIER) cc_final: -0.1054 (m) REVERT: V 229 GLN cc_start: 0.1605 (pm20) cc_final: 0.1013 (pp30) REVERT: V 239 GLU cc_start: 0.2299 (OUTLIER) cc_final: 0.1088 (pt0) REVERT: V 255 GLU cc_start: 0.3145 (OUTLIER) cc_final: 0.2681 (tp30) REVERT: V 267 ASP cc_start: 0.1145 (OUTLIER) cc_final: 0.0642 (m-30) REVERT: V 270 LYS cc_start: 0.1166 (OUTLIER) cc_final: 0.0686 (ptpt) outliers start: 416 outliers final: 84 residues processed: 1547 average time/residue: 0.6455 time to fit residues: 1597.8367 Evaluate side-chains 705 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 585 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 38 LYS Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 174 ASN Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 207 GLU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 274 ARG Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 309 MET Chi-restraints excluded: chain K residue 310 GLN Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 326 PHE Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 374 ASP Chi-restraints excluded: chain K residue 379 ARG Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain M residue 192 TYR Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 407 THR Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 407 VAL Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 267 GLU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 165 LYS Chi-restraints excluded: chain Q residue 181 GLN Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 211 THR Chi-restraints excluded: chain Q residue 237 ASP Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain Q residue 316 HIS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 215 TYR Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 374 ARG Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 91 LYS Chi-restraints excluded: chain V residue 120 GLU Chi-restraints excluded: chain V residue 134 GLN Chi-restraints excluded: chain V residue 156 GLU Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 206 ARG Chi-restraints excluded: chain V residue 217 VAL Chi-restraints excluded: chain V residue 222 HIS Chi-restraints excluded: chain V residue 223 GLU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain V residue 265 SER Chi-restraints excluded: chain V residue 267 ASP Chi-restraints excluded: chain V residue 270 LYS Chi-restraints excluded: chain V residue 271 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 553 optimal weight: 8.9990 chunk 496 optimal weight: 4.9990 chunk 275 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 334 optimal weight: 0.7980 chunk 265 optimal weight: 0.7980 chunk 513 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 312 optimal weight: 4.9990 chunk 382 optimal weight: 4.9990 chunk 594 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 60 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN G 85 GLN G 108 ASN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 855 HIS I 967 HIS I1896 GLN I1963 GLN I1964 GLN I2046 GLN ** I2067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 HIS K 156 HIS K 174 ASN ** K 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 310 GLN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN ** M 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 HIS ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 GLN N 277 ASN N 302 HIS N 329 ASN P 146 GLN P 226 GLN P 240 HIS ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 313 ASN P 447 GLN Q 229 HIS Q 284 ASN Q 408 GLN Q 429 HIS S 137 GLN T 143 HIS U 101 HIS U 173 HIS U 296 ASN U 353 GLN ** V 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 204 ASN V 269 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4896 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 58334 Z= 0.286 Angle : 0.733 14.332 80061 Z= 0.385 Chirality : 0.046 0.421 9018 Planarity : 0.006 0.079 9229 Dihedral : 22.388 159.476 10594 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.48 % Favored : 94.17 % Rotamer: Outliers : 4.79 % Allowed : 14.48 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.10), residues: 6298 helix: -0.42 (0.09), residues: 2917 sheet: -0.32 (0.18), residues: 740 loop : -1.52 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 277 HIS 0.016 0.001 HIS I 102 PHE 0.046 0.002 PHE A 26 TYR 0.025 0.002 TYR C 54 ARG 0.014 0.001 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 613 time to evaluate : 4.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4420 (OUTLIER) cc_final: 0.4204 (mt) REVERT: E 74 LYS cc_start: 0.7702 (mttt) cc_final: 0.7190 (mtpt) REVERT: F 28 ARG cc_start: 0.1192 (OUTLIER) cc_final: 0.0293 (mmt180) REVERT: G 81 ASP cc_start: 0.5451 (m-30) cc_final: 0.5243 (m-30) REVERT: I 847 LYS cc_start: 0.4844 (mmtm) cc_final: 0.4587 (mppt) REVERT: I 895 MET cc_start: 0.7163 (tpp) cc_final: 0.6747 (tpt) REVERT: I 923 PHE cc_start: 0.6962 (p90) cc_final: 0.6749 (p90) REVERT: I 2036 ARG cc_start: 0.6792 (mmm160) cc_final: 0.6330 (mtm110) REVERT: I 2073 ASP cc_start: 0.6663 (t0) cc_final: 0.6437 (m-30) REVERT: J 187 LEU cc_start: 0.6485 (mt) cc_final: 0.5939 (tp) REVERT: K 64 TYR cc_start: 0.1738 (m-80) cc_final: 0.1152 (m-10) REVERT: K 138 ASP cc_start: 0.5665 (OUTLIER) cc_final: 0.5308 (p0) REVERT: K 185 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7032 (mtpt) REVERT: K 220 MET cc_start: 0.6749 (mmm) cc_final: 0.6420 (mmm) REVERT: K 229 GLU cc_start: 0.5861 (OUTLIER) cc_final: 0.5481 (pm20) REVERT: K 238 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.5997 (pp) REVERT: K 292 MET cc_start: 0.7522 (pmm) cc_final: 0.6559 (ptp) REVERT: K 383 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: L 100 ASN cc_start: 0.6663 (p0) cc_final: 0.6424 (p0) REVERT: M 181 GLN cc_start: 0.8393 (mt0) cc_final: 0.8005 (mm-40) REVERT: M 192 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7655 (p90) REVERT: M 242 ASP cc_start: 0.7257 (t0) cc_final: 0.6670 (m-30) REVERT: M 268 LYS cc_start: 0.6759 (mtpt) cc_final: 0.6446 (mtpt) REVERT: M 323 ILE cc_start: 0.8589 (pt) cc_final: 0.8198 (mt) REVERT: M 346 SER cc_start: 0.8952 (m) cc_final: 0.8303 (t) REVERT: M 364 MET cc_start: 0.8213 (ptp) cc_final: 0.7956 (mtm) REVERT: N 132 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8243 (mtmm) REVERT: N 267 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8139 (mp0) REVERT: N 381 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7204 (mp0) REVERT: N 436 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7281 (tm-30) REVERT: O 18 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.6491 (t-90) REVERT: O 265 LYS cc_start: 0.7256 (tptt) cc_final: 0.7047 (tptt) REVERT: O 323 ILE cc_start: 0.8231 (pt) cc_final: 0.7784 (mt) REVERT: P 168 MET cc_start: 0.7902 (ptm) cc_final: 0.7614 (ptp) REVERT: P 188 GLN cc_start: 0.8148 (pt0) cc_final: 0.7822 (pm20) REVERT: P 232 LEU cc_start: 0.7711 (tp) cc_final: 0.7470 (tp) REVERT: P 246 GLU cc_start: 0.7386 (tt0) cc_final: 0.7120 (mt-10) REVERT: P 274 GLU cc_start: 0.7145 (mp0) cc_final: 0.6601 (mt-10) REVERT: P 284 ARG cc_start: 0.6758 (ttt90) cc_final: 0.6523 (ttp-110) REVERT: Q 61 MET cc_start: 0.8701 (mmm) cc_final: 0.8225 (mmm) REVERT: Q 165 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7241 (tptp) REVERT: Q 170 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7932 (mp) REVERT: Q 237 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7720 (p0) REVERT: Q 308 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6721 (t70) REVERT: R 67 LYS cc_start: 0.8069 (mttt) cc_final: 0.7554 (mmtt) REVERT: R 88 MET cc_start: 0.8176 (mmm) cc_final: 0.7764 (mmt) REVERT: R 90 MET cc_start: 0.7842 (mtp) cc_final: 0.7381 (mtm) REVERT: R 207 ARG cc_start: 0.5868 (ttm170) cc_final: 0.5620 (ttm170) REVERT: R 246 GLU cc_start: 0.4528 (OUTLIER) cc_final: 0.3225 (pt0) REVERT: S 44 MET cc_start: 0.0203 (mtp) cc_final: -0.0673 (tpp) REVERT: S 229 THR cc_start: 0.2936 (m) cc_final: 0.2525 (p) REVERT: T 140 MET cc_start: 0.2571 (mmm) cc_final: 0.1673 (mmp) REVERT: U 28 ARG cc_start: 0.2762 (mmm160) cc_final: 0.2247 (mmm160) REVERT: U 227 MET cc_start: 0.0794 (mmt) cc_final: -0.0961 (ttp) REVERT: U 330 ILE cc_start: 0.0516 (OUTLIER) cc_final: -0.0086 (tt) REVERT: V 90 LYS cc_start: 0.3311 (pttm) cc_final: 0.1901 (mtmt) REVERT: V 91 LYS cc_start: 0.0232 (OUTLIER) cc_final: -0.1633 (mptt) REVERT: V 223 GLU cc_start: 0.0442 (OUTLIER) cc_final: -0.0054 (tp30) REVERT: V 239 GLU cc_start: 0.2927 (OUTLIER) cc_final: 0.1859 (pt0) REVERT: V 255 GLU cc_start: 0.2925 (OUTLIER) cc_final: 0.2338 (tp30) REVERT: V 267 ASP cc_start: 0.0970 (OUTLIER) cc_final: 0.0266 (m-30) REVERT: V 270 LYS cc_start: 0.1626 (OUTLIER) cc_final: 0.1194 (ptpt) REVERT: W 128 MET cc_start: 0.2863 (ptm) cc_final: 0.0118 (mmp) outliers start: 262 outliers final: 112 residues processed: 821 average time/residue: 0.5418 time to fit residues: 747.6863 Evaluate side-chains 622 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 488 time to evaluate : 4.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 884 THR Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 969 LEU Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 1980 MET Chi-restraints excluded: chain I residue 1989 SER Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2196 PHE Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 374 ASP Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 129 GLU Chi-restraints excluded: chain M residue 192 TYR Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 407 VAL Chi-restraints excluded: chain O residue 416 LEU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 267 GLU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 431 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 165 LYS Chi-restraints excluded: chain Q residue 170 LEU Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 237 ASP Chi-restraints excluded: chain Q residue 269 THR Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain Q residue 316 HIS Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 132 MET Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 96 TRP Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 91 LYS Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 223 GLU Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain V residue 267 ASP Chi-restraints excluded: chain V residue 270 LYS Chi-restraints excluded: chain V residue 271 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 330 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 495 optimal weight: 30.0000 chunk 405 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 595 optimal weight: 8.9990 chunk 643 optimal weight: 10.0000 chunk 530 optimal weight: 10.0000 chunk 590 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 478 optimal weight: 50.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN B 60 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** I 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 702 GLN ** I 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 795 HIS ** I2067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I2084 HIS I2153 HIS ** J 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 HIS ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 HIS ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 GLN M 305 HIS ** M 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 392 ASN ** P 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 404 GLN S 137 GLN T 105 HIS T 251 HIS T 408 GLN U 296 ASN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5007 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 58334 Z= 0.358 Angle : 0.720 11.870 80061 Z= 0.375 Chirality : 0.047 0.610 9018 Planarity : 0.006 0.077 9229 Dihedral : 21.965 158.796 10457 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.59 % Favored : 94.13 % Rotamer: Outliers : 4.54 % Allowed : 16.33 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.10), residues: 6298 helix: -0.21 (0.09), residues: 2917 sheet: -0.38 (0.18), residues: 780 loop : -1.49 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP T 250 HIS 0.010 0.001 HIS I 102 PHE 0.027 0.002 PHE I 923 TYR 0.027 0.002 TYR A 58 ARG 0.010 0.001 ARG I 931 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 523 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.5144 (OUTLIER) cc_final: 0.4720 (tm-30) REVERT: A 93 GLU cc_start: 0.5433 (pm20) cc_final: 0.4752 (pm20) REVERT: E 58 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8236 (mm) REVERT: I 144 MET cc_start: 0.0024 (ppp) cc_final: -0.1732 (tmm) REVERT: I 855 HIS cc_start: 0.6724 (m-70) cc_final: 0.6382 (m-70) REVERT: I 895 MET cc_start: 0.7461 (tpp) cc_final: 0.7065 (tpt) REVERT: I 923 PHE cc_start: 0.6954 (p90) cc_final: 0.6690 (p90) REVERT: I 941 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.6138 (tp) REVERT: I 2036 ARG cc_start: 0.6801 (mmm160) cc_final: 0.6139 (mtm110) REVERT: I 2073 ASP cc_start: 0.6729 (t0) cc_final: 0.6436 (m-30) REVERT: K 1 MET cc_start: 0.3164 (pp-130) cc_final: 0.2212 (pp-130) REVERT: K 12 ASN cc_start: 0.6659 (OUTLIER) cc_final: 0.5098 (p0) REVERT: K 138 ASP cc_start: 0.6126 (OUTLIER) cc_final: 0.5742 (p0) REVERT: K 185 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7599 (mtpt) REVERT: K 196 MET cc_start: 0.5773 (ptm) cc_final: 0.5333 (ptm) REVERT: K 202 ILE cc_start: 0.6090 (OUTLIER) cc_final: 0.5826 (tt) REVERT: K 229 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5577 (pm20) REVERT: K 314 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.5494 (p90) REVERT: K 375 MET cc_start: 0.6595 (tmm) cc_final: 0.6239 (tmm) REVERT: M 242 ASP cc_start: 0.7418 (t0) cc_final: 0.6834 (m-30) REVERT: M 243 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6416 (mp) REVERT: M 308 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.5966 (t0) REVERT: M 323 ILE cc_start: 0.8606 (pt) cc_final: 0.8238 (mt) REVERT: M 346 SER cc_start: 0.8926 (m) cc_final: 0.8277 (t) REVERT: N 354 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7790 (pp) REVERT: N 436 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7278 (tm-30) REVERT: O 18 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.5177 (t-90) REVERT: O 249 ARG cc_start: 0.7282 (mtp85) cc_final: 0.7045 (mtp85) REVERT: O 265 LYS cc_start: 0.7772 (tptt) cc_final: 0.7442 (tppt) REVERT: O 270 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: O 323 ILE cc_start: 0.8303 (pt) cc_final: 0.7840 (mt) REVERT: O 342 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: O 359 MET cc_start: 0.7791 (mtm) cc_final: 0.7385 (mtm) REVERT: P 168 MET cc_start: 0.7478 (ptm) cc_final: 0.6707 (ptp) REVERT: P 188 GLN cc_start: 0.8203 (pt0) cc_final: 0.7874 (pm20) REVERT: P 267 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: P 284 ARG cc_start: 0.6919 (ttt90) cc_final: 0.6589 (ttp-110) REVERT: Q 61 MET cc_start: 0.8758 (mmm) cc_final: 0.8282 (mmm) REVERT: Q 64 ARG cc_start: 0.7374 (mmm160) cc_final: 0.6971 (mmm-85) REVERT: Q 165 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7054 (tmtt) REVERT: Q 169 GLN cc_start: 0.6864 (mt0) cc_final: 0.6564 (mm-40) REVERT: Q 237 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7857 (p0) REVERT: Q 308 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.6426 (t70) REVERT: Q 364 MET cc_start: 0.7390 (mmm) cc_final: 0.6987 (mmm) REVERT: R 67 LYS cc_start: 0.8250 (mttt) cc_final: 0.7649 (mmtt) REVERT: R 88 MET cc_start: 0.8178 (mmm) cc_final: 0.7790 (mmt) REVERT: R 246 GLU cc_start: 0.4811 (OUTLIER) cc_final: 0.3505 (pt0) REVERT: R 271 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: R 364 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6497 (tm-30) REVERT: R 365 LYS cc_start: 0.7535 (mmmt) cc_final: 0.7144 (mmmt) REVERT: S 44 MET cc_start: 0.0128 (mtp) cc_final: -0.0750 (tpp) REVERT: S 190 MET cc_start: 0.2421 (tpp) cc_final: 0.1280 (mmm) REVERT: S 229 THR cc_start: 0.2896 (m) cc_final: 0.2455 (p) REVERT: S 354 GLN cc_start: 0.3861 (pm20) cc_final: 0.2428 (tp40) REVERT: T 105 HIS cc_start: 0.2982 (OUTLIER) cc_final: 0.2550 (t-170) REVERT: T 140 MET cc_start: 0.1644 (mmm) cc_final: 0.1034 (mmp) REVERT: T 409 MET cc_start: 0.4342 (OUTLIER) cc_final: 0.3823 (ttt) REVERT: U 82 MET cc_start: 0.1559 (tpp) cc_final: 0.1305 (ttt) REVERT: U 227 MET cc_start: 0.1149 (mmt) cc_final: -0.0716 (ttp) REVERT: U 330 ILE cc_start: 0.0750 (OUTLIER) cc_final: 0.0132 (tt) REVERT: V 90 LYS cc_start: 0.3205 (pttm) cc_final: 0.2317 (mtmt) REVERT: V 239 GLU cc_start: 0.2551 (OUTLIER) cc_final: 0.1495 (pt0) REVERT: V 255 GLU cc_start: 0.2445 (OUTLIER) cc_final: 0.2162 (tt0) REVERT: V 267 ASP cc_start: 0.0949 (OUTLIER) cc_final: 0.0313 (m-30) outliers start: 248 outliers final: 140 residues processed: 725 average time/residue: 0.5273 time to fit residues: 651.1417 Evaluate side-chains 607 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 440 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 25 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 232 HIS Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 657 LEU Chi-restraints excluded: chain I residue 703 LYS Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 754 PHE Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 900 VAL Chi-restraints excluded: chain I residue 941 ILE Chi-restraints excluded: chain I residue 969 LEU Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 1989 SER Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 274 ARG Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 333 VAL Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 374 ASP Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 129 GLU Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 171 ILE Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 283 TRP Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain N residue 447 GLN Chi-restraints excluded: chain O residue 15 ILE Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 139 THR Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 407 VAL Chi-restraints excluded: chain O residue 416 LEU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 113 MET Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 267 GLU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 431 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 165 LYS Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 237 ASP Chi-restraints excluded: chain Q residue 269 THR Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain Q residue 316 HIS Chi-restraints excluded: chain Q residue 353 ASP Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 271 GLU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 69 TYR Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 132 MET Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 105 HIS Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain T residue 409 MET Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 214 LYS Chi-restraints excluded: chain V residue 229 GLN Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 245 GLU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain V residue 267 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 588 optimal weight: 5.9990 chunk 448 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 284 optimal weight: 5.9990 chunk 400 optimal weight: 0.9980 chunk 598 optimal weight: 5.9990 chunk 633 optimal weight: 6.9990 chunk 312 optimal weight: 1.9990 chunk 566 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 60 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** I 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 780 ASN I1963 GLN ** I2067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN K 156 HIS ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 272 ASN ** K 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 ASN ** M 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 137 GLN V 180 HIS V 204 ASN W 29 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5012 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 58334 Z= 0.263 Angle : 0.649 10.938 80061 Z= 0.337 Chirality : 0.043 0.295 9018 Planarity : 0.005 0.075 9229 Dihedral : 21.667 158.448 10420 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.56 % Favored : 94.17 % Rotamer: Outliers : 4.61 % Allowed : 17.10 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.10), residues: 6298 helix: 0.04 (0.10), residues: 2906 sheet: -0.30 (0.18), residues: 806 loop : -1.40 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 96 HIS 0.031 0.001 HIS T 105 PHE 0.030 0.002 PHE N 261 TYR 0.019 0.001 TYR K 261 ARG 0.006 0.000 ARG N 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 482 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7238 (mm) REVERT: E 58 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8165 (mm) REVERT: I 144 MET cc_start: -0.0041 (ppp) cc_final: -0.1840 (tmm) REVERT: I 672 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8366 (mt) REVERT: I 754 PHE cc_start: 0.7119 (p90) cc_final: 0.6839 (p90) REVERT: I 849 MET cc_start: 0.5957 (tpt) cc_final: 0.5610 (tpt) REVERT: I 855 HIS cc_start: 0.6853 (m-70) cc_final: 0.6402 (m-70) REVERT: I 895 MET cc_start: 0.7506 (tpp) cc_final: 0.7269 (tpt) REVERT: I 923 PHE cc_start: 0.7157 (p90) cc_final: 0.6780 (p90) REVERT: I 2036 ARG cc_start: 0.6732 (mmm160) cc_final: 0.6133 (mtm110) REVERT: I 2067 GLN cc_start: 0.5547 (OUTLIER) cc_final: 0.5251 (mp10) REVERT: I 2073 ASP cc_start: 0.6699 (t0) cc_final: 0.6386 (m-30) REVERT: J 187 LEU cc_start: 0.6632 (mt) cc_final: 0.6099 (tp) REVERT: K 1 MET cc_start: 0.3003 (pp-130) cc_final: 0.2418 (ppp) REVERT: K 12 ASN cc_start: 0.6481 (OUTLIER) cc_final: 0.5243 (p0) REVERT: K 83 MET cc_start: 0.4758 (mmp) cc_final: 0.4551 (mmm) REVERT: K 138 ASP cc_start: 0.6302 (OUTLIER) cc_final: 0.5843 (p0) REVERT: K 154 PHE cc_start: 0.5343 (OUTLIER) cc_final: 0.4777 (m-10) REVERT: K 229 GLU cc_start: 0.5808 (OUTLIER) cc_final: 0.5607 (pm20) REVERT: K 314 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.5205 (p90) REVERT: K 375 MET cc_start: 0.6222 (tmm) cc_final: 0.5910 (tmm) REVERT: M 242 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6688 (m-30) REVERT: M 268 LYS cc_start: 0.7298 (mttm) cc_final: 0.6940 (mmtp) REVERT: M 323 ILE cc_start: 0.8646 (pt) cc_final: 0.8276 (mt) REVERT: M 346 SER cc_start: 0.8824 (m) cc_final: 0.8181 (t) REVERT: N 119 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6105 (mt) REVERT: N 132 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8184 (mmtm) REVERT: N 269 LYS cc_start: 0.7372 (pttt) cc_final: 0.6896 (ptpp) REVERT: N 329 ASN cc_start: 0.8114 (m-40) cc_final: 0.7894 (m110) REVERT: N 354 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7930 (pp) REVERT: N 400 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.5891 (mtm180) REVERT: O 18 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.5732 (t-90) REVERT: O 223 LEU cc_start: 0.7647 (tp) cc_final: 0.7305 (tp) REVERT: O 265 LYS cc_start: 0.7727 (tptt) cc_final: 0.7475 (tptt) REVERT: O 270 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: O 323 ILE cc_start: 0.8378 (pt) cc_final: 0.7902 (mt) REVERT: O 342 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: O 359 MET cc_start: 0.7746 (mtm) cc_final: 0.7342 (mtm) REVERT: P 168 MET cc_start: 0.7702 (ptm) cc_final: 0.7173 (ptp) REVERT: P 188 GLN cc_start: 0.8165 (pt0) cc_final: 0.7869 (pm20) REVERT: P 267 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: P 284 ARG cc_start: 0.6563 (ttt90) cc_final: 0.6317 (ttp-110) REVERT: P 349 ASP cc_start: 0.8204 (t0) cc_final: 0.7673 (p0) REVERT: P 448 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.6973 (t0) REVERT: Q 61 MET cc_start: 0.8760 (mmm) cc_final: 0.8322 (mmm) REVERT: Q 165 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7040 (tmtt) REVERT: Q 308 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6347 (t70) REVERT: Q 364 MET cc_start: 0.7412 (mmm) cc_final: 0.7045 (mmm) REVERT: Q 396 GLU cc_start: 0.8221 (tp30) cc_final: 0.7820 (tt0) REVERT: R 67 LYS cc_start: 0.8177 (mttt) cc_final: 0.7540 (mmtt) REVERT: R 88 MET cc_start: 0.8201 (mmm) cc_final: 0.7945 (mmm) REVERT: R 235 ARG cc_start: 0.8031 (mtp-110) cc_final: 0.7386 (mtt180) REVERT: R 246 GLU cc_start: 0.4683 (OUTLIER) cc_final: 0.3477 (pt0) REVERT: R 253 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.7268 (ttm110) REVERT: R 346 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6933 (pt) REVERT: R 364 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6962 (tm-30) REVERT: S 44 MET cc_start: 0.0177 (mtp) cc_final: -0.0774 (tpp) REVERT: S 190 MET cc_start: 0.2814 (tpp) cc_final: 0.1784 (mmm) REVERT: S 229 THR cc_start: 0.2863 (m) cc_final: 0.2423 (p) REVERT: S 305 MET cc_start: 0.2610 (mmm) cc_final: 0.2196 (mmm) REVERT: S 354 GLN cc_start: 0.3882 (pm20) cc_final: 0.2396 (tp40) REVERT: T 39 THR cc_start: 0.0879 (m) cc_final: 0.0319 (m) REVERT: U 28 ARG cc_start: 0.2643 (mmm160) cc_final: 0.2177 (mmm160) REVERT: U 227 MET cc_start: 0.1117 (mmt) cc_final: -0.0740 (ttp) REVERT: U 330 ILE cc_start: 0.0862 (OUTLIER) cc_final: 0.0235 (tt) REVERT: V 239 GLU cc_start: 0.2769 (OUTLIER) cc_final: 0.1610 (pt0) REVERT: V 267 ASP cc_start: 0.1102 (OUTLIER) cc_final: 0.0719 (m-30) REVERT: W 151 MET cc_start: 0.2243 (ttt) cc_final: 0.0844 (tpp) outliers start: 252 outliers final: 151 residues processed: 692 average time/residue: 0.5296 time to fit residues: 629.4916 Evaluate side-chains 623 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 446 time to evaluate : 4.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 25 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 672 ILE Chi-restraints excluded: chain I residue 703 LYS Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 884 THR Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 900 VAL Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 969 LEU Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 1989 SER Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2037 LEU Chi-restraints excluded: chain I residue 2067 GLN Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 333 VAL Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 374 ASP Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 129 GLU Chi-restraints excluded: chain M residue 242 ASP Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 171 ILE Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 283 TRP Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain N residue 447 GLN Chi-restraints excluded: chain O residue 15 ILE Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 139 THR Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 345 THR Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 416 LEU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 113 MET Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 267 GLU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 375 CYS Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 431 SER Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 165 LYS Chi-restraints excluded: chain Q residue 170 LEU Chi-restraints excluded: chain Q residue 221 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain Q residue 353 ASP Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 271 GLU Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain S residue 69 TYR Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 351 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 109 MET Chi-restraints excluded: chain T residue 327 HIS Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 205 GLU Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 214 LYS Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 229 GLN Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 267 ASP Chi-restraints excluded: chain V residue 271 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 527 optimal weight: 30.0000 chunk 359 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 471 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 540 optimal weight: 9.9990 chunk 437 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 323 optimal weight: 4.9990 chunk 568 optimal weight: 30.0000 chunk 159 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN E 31 HIS G 39 HIS H 93 GLN I 623 HIS ** I 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 HIS I1991 HIS ** I2067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I2082 HIS J 162 HIS K 110 ASN K 139 ASN K 200 HIS K 230 ASN K 283 ASN K 303 GLN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 420 ASN N 275 GLN O 348 HIS ** O 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 344 HIS Q 348 HIS S 137 GLN T 81 ASN T 105 HIS U 88 HIS V 240 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5102 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 58334 Z= 0.437 Angle : 0.744 11.030 80061 Z= 0.386 Chirality : 0.047 0.412 9018 Planarity : 0.006 0.083 9229 Dihedral : 21.613 154.895 10405 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.24 % Favored : 93.52 % Rotamer: Outliers : 5.50 % Allowed : 17.56 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.10), residues: 6298 helix: -0.15 (0.09), residues: 2918 sheet: -0.33 (0.18), residues: 796 loop : -1.55 (0.11), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J 277 HIS 0.011 0.002 HIS I2060 PHE 0.033 0.002 PHE N 261 TYR 0.034 0.002 TYR A 58 ARG 0.008 0.001 ARG N 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 460 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 VAL cc_start: 0.7692 (t) cc_final: 0.7456 (t) REVERT: E 58 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8009 (mm) REVERT: F 59 MET cc_start: 0.8431 (mmt) cc_final: 0.8100 (mmt) REVERT: I 144 MET cc_start: 0.0219 (ppp) cc_final: -0.1265 (tmm) REVERT: I 742 TYR cc_start: 0.7080 (m-80) cc_final: 0.5780 (m-80) REVERT: I 849 MET cc_start: 0.6108 (tpt) cc_final: 0.5760 (tpt) REVERT: I 895 MET cc_start: 0.7511 (tpp) cc_final: 0.7219 (tpt) REVERT: I 2036 ARG cc_start: 0.6902 (mmm160) cc_final: 0.6408 (mtm110) REVERT: I 2067 GLN cc_start: 0.5515 (OUTLIER) cc_final: 0.5269 (mp10) REVERT: I 2073 ASP cc_start: 0.6743 (t0) cc_final: 0.6480 (m-30) REVERT: J 187 LEU cc_start: 0.6632 (mt) cc_final: 0.6393 (mm) REVERT: K 1 MET cc_start: 0.2014 (pp-130) cc_final: 0.1333 (ppp) REVERT: K 12 ASN cc_start: 0.6967 (OUTLIER) cc_final: 0.6752 (t0) REVERT: K 64 TYR cc_start: 0.2379 (m-80) cc_final: 0.1790 (m-80) REVERT: K 117 TYR cc_start: 0.5049 (m-80) cc_final: 0.4678 (m-10) REVERT: K 138 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6398 (p0) REVERT: K 229 GLU cc_start: 0.5611 (OUTLIER) cc_final: 0.5410 (pm20) REVERT: K 255 MET cc_start: 0.1959 (mmm) cc_final: 0.1637 (mmm) REVERT: K 313 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.5832 (t80) REVERT: K 314 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.5699 (p90) REVERT: K 325 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6580 (mm) REVERT: K 375 MET cc_start: 0.6156 (tmm) cc_final: 0.5840 (tmm) REVERT: M 234 ILE cc_start: 0.8249 (tp) cc_final: 0.8042 (tp) REVERT: M 242 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6712 (m-30) REVERT: M 243 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6471 (mp) REVERT: M 268 LYS cc_start: 0.7501 (mttm) cc_final: 0.7081 (mmtp) REVERT: M 323 ILE cc_start: 0.8594 (pt) cc_final: 0.8312 (mt) REVERT: N 132 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8159 (mmtm) REVERT: N 274 GLU cc_start: 0.6960 (tt0) cc_final: 0.6509 (tm-30) REVERT: N 354 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7788 (pp) REVERT: N 400 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.6033 (mtm180) REVERT: O 18 HIS cc_start: 0.7039 (OUTLIER) cc_final: 0.5420 (t-90) REVERT: O 270 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7801 (pm20) REVERT: O 323 ILE cc_start: 0.8372 (pt) cc_final: 0.7816 (mt) REVERT: O 342 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: O 359 MET cc_start: 0.7832 (mtm) cc_final: 0.7379 (mtm) REVERT: P 19 ILE cc_start: 0.5246 (OUTLIER) cc_final: 0.4764 (tt) REVERT: P 168 MET cc_start: 0.7628 (ptm) cc_final: 0.7112 (ptp) REVERT: P 188 GLN cc_start: 0.8148 (pt0) cc_final: 0.7903 (pm20) REVERT: P 264 ASP cc_start: 0.4915 (OUTLIER) cc_final: 0.4195 (p0) REVERT: P 284 ARG cc_start: 0.6646 (ttt90) cc_final: 0.6350 (ttp-110) REVERT: P 330 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8015 (ptp90) REVERT: P 349 ASP cc_start: 0.8204 (t0) cc_final: 0.7800 (p0) REVERT: P 448 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7057 (t0) REVERT: Q 61 MET cc_start: 0.8922 (mmm) cc_final: 0.8145 (mmm) REVERT: Q 192 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.5424 (t80) REVERT: Q 308 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6519 (t70) REVERT: Q 364 MET cc_start: 0.7362 (mmm) cc_final: 0.6963 (mmm) REVERT: Q 396 GLU cc_start: 0.8278 (tp30) cc_final: 0.7874 (tt0) REVERT: R 67 LYS cc_start: 0.8100 (mttt) cc_final: 0.7564 (mmtt) REVERT: R 88 MET cc_start: 0.7955 (mmm) cc_final: 0.7642 (mmt) REVERT: R 168 MET cc_start: 0.6467 (ptp) cc_final: 0.6123 (ptp) REVERT: R 207 ARG cc_start: 0.6262 (ttm170) cc_final: 0.5949 (ttm170) REVERT: R 246 GLU cc_start: 0.4735 (OUTLIER) cc_final: 0.4271 (pp20) REVERT: R 346 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6663 (pt) REVERT: R 364 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6978 (tm-30) REVERT: S 44 MET cc_start: 0.0345 (mtp) cc_final: -0.0500 (tpp) REVERT: S 190 MET cc_start: 0.2648 (tpp) cc_final: 0.1716 (mmm) REVERT: S 229 THR cc_start: 0.2706 (m) cc_final: 0.2248 (p) REVERT: S 354 GLN cc_start: 0.4107 (OUTLIER) cc_final: 0.2654 (tp40) REVERT: T 82 MET cc_start: -0.0800 (mmm) cc_final: -0.1108 (mmm) REVERT: U 227 MET cc_start: 0.0936 (mmt) cc_final: -0.0841 (ttp) REVERT: U 330 ILE cc_start: 0.0870 (OUTLIER) cc_final: 0.0138 (tt) REVERT: V 239 GLU cc_start: 0.2789 (OUTLIER) cc_final: 0.1607 (pt0) REVERT: W 128 MET cc_start: 0.3911 (ptm) cc_final: 0.2924 (mtm) REVERT: W 142 MET cc_start: 0.0948 (mmp) cc_final: 0.0671 (mmt) outliers start: 301 outliers final: 195 residues processed: 706 average time/residue: 0.5215 time to fit residues: 633.2775 Evaluate side-chains 647 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 425 time to evaluate : 4.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 232 HIS Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 653 THR Chi-restraints excluded: chain I residue 657 LEU Chi-restraints excluded: chain I residue 678 VAL Chi-restraints excluded: chain I residue 679 MET Chi-restraints excluded: chain I residue 703 LYS Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 727 LEU Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 774 THR Chi-restraints excluded: chain I residue 807 PHE Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 856 VAL Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 900 VAL Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 969 LEU Chi-restraints excluded: chain I residue 974 LEU Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 1989 SER Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2037 LEU Chi-restraints excluded: chain I residue 2067 GLN Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2118 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 303 GLN Chi-restraints excluded: chain K residue 313 PHE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 333 VAL Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 374 ASP Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 242 ASP Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 355 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 171 ILE Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 283 TRP Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain N residue 447 GLN Chi-restraints excluded: chain O residue 15 ILE Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 345 THR Chi-restraints excluded: chain O residue 362 ARG Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 407 VAL Chi-restraints excluded: chain O residue 416 LEU Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 113 MET Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 264 ASP Chi-restraints excluded: chain P residue 267 GLU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 330 ARG Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 375 CYS Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 431 SER Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 96 MET Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 221 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain Q residue 316 HIS Chi-restraints excluded: chain Q residue 323 ILE Chi-restraints excluded: chain Q residue 353 ASP Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 271 GLU Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 351 THR Chi-restraints excluded: chain S residue 354 GLN Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 96 TRP Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 201 THR Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 272 CYS Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 214 LYS Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 229 GLN Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 213 optimal weight: 0.0020 chunk 570 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 371 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 633 optimal weight: 6.9990 chunk 526 optimal weight: 9.9990 chunk 293 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 209 optimal weight: 0.1980 chunk 332 optimal weight: 0.8980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN I 659 HIS I2067 GLN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 275 GLN ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN T 105 HIS T 383 ASN V 240 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5023 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 58334 Z= 0.167 Angle : 0.606 10.090 80061 Z= 0.313 Chirality : 0.041 0.304 9018 Planarity : 0.004 0.074 9229 Dihedral : 21.320 155.066 10398 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.27 % Favored : 94.52 % Rotamer: Outliers : 3.69 % Allowed : 19.29 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.10), residues: 6298 helix: 0.27 (0.10), residues: 2924 sheet: -0.31 (0.18), residues: 793 loop : -1.33 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 277 HIS 0.010 0.001 HIS M 316 PHE 0.027 0.001 PHE I 923 TYR 0.035 0.001 TYR K 17 ARG 0.009 0.000 ARG N 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 497 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 VAL cc_start: 0.7660 (t) cc_final: 0.7428 (t) REVERT: E 58 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8073 (mm) REVERT: F 59 MET cc_start: 0.8357 (mmt) cc_final: 0.8082 (mmt) REVERT: I 144 MET cc_start: -0.0691 (ppp) cc_final: -0.1967 (tmm) REVERT: I 198 MET cc_start: 0.3416 (ptt) cc_final: 0.2919 (ptt) REVERT: I 742 TYR cc_start: 0.7326 (m-80) cc_final: 0.5706 (m-80) REVERT: I 895 MET cc_start: 0.7616 (tpp) cc_final: 0.7382 (tpt) REVERT: I 2028 MET cc_start: 0.8902 (ttm) cc_final: 0.8653 (mtp) REVERT: I 2036 ARG cc_start: 0.6811 (mmm160) cc_final: 0.6291 (mtm110) REVERT: I 2067 GLN cc_start: 0.5962 (OUTLIER) cc_final: 0.5596 (mp10) REVERT: I 2073 ASP cc_start: 0.6670 (t0) cc_final: 0.6410 (m-30) REVERT: J 187 LEU cc_start: 0.6444 (mt) cc_final: 0.6166 (mm) REVERT: K 1 MET cc_start: 0.2140 (OUTLIER) cc_final: 0.1436 (ppp) REVERT: K 64 TYR cc_start: 0.2142 (m-80) cc_final: 0.1608 (m-10) REVERT: K 138 ASP cc_start: 0.6550 (OUTLIER) cc_final: 0.6326 (p0) REVERT: K 196 MET cc_start: 0.5826 (tmm) cc_final: 0.5526 (tmm) REVERT: K 220 MET cc_start: 0.7118 (mtm) cc_final: 0.6601 (mtt) REVERT: K 325 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6431 (mm) REVERT: K 375 MET cc_start: 0.5857 (tmm) cc_final: 0.5628 (tmm) REVERT: M 242 ASP cc_start: 0.7188 (t0) cc_final: 0.6570 (m-30) REVERT: M 260 MET cc_start: 0.6261 (mpp) cc_final: 0.6047 (mpp) REVERT: M 268 LYS cc_start: 0.7457 (mttm) cc_final: 0.7047 (mmtp) REVERT: M 308 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.5766 (t0) REVERT: M 323 ILE cc_start: 0.8637 (pt) cc_final: 0.8326 (mt) REVERT: N 132 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8149 (mmtm) REVERT: N 269 LYS cc_start: 0.7306 (pttt) cc_final: 0.6855 (ptpp) REVERT: N 354 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7929 (pp) REVERT: N 400 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.5944 (mtm180) REVERT: O 18 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.5351 (t-90) REVERT: O 249 ARG cc_start: 0.6348 (mmm160) cc_final: 0.6147 (mmm160) REVERT: O 265 LYS cc_start: 0.7420 (tptt) cc_final: 0.7186 (mmtt) REVERT: O 270 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: O 323 ILE cc_start: 0.8383 (pt) cc_final: 0.7868 (mt) REVERT: O 342 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: O 359 MET cc_start: 0.7720 (mtm) cc_final: 0.7299 (mtm) REVERT: P 19 ILE cc_start: 0.5065 (mt) cc_final: 0.4609 (tt) REVERT: P 46 MET cc_start: 0.8504 (tpp) cc_final: 0.8139 (mtp) REVERT: P 168 MET cc_start: 0.7694 (ptm) cc_final: 0.7448 (ptp) REVERT: P 284 ARG cc_start: 0.6689 (ttt90) cc_final: 0.6307 (ttp-110) REVERT: P 349 ASP cc_start: 0.8161 (t0) cc_final: 0.7898 (t0) REVERT: P 382 MET cc_start: 0.8350 (mtp) cc_final: 0.7934 (mtm) REVERT: P 448 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6446 (t0) REVERT: Q 61 MET cc_start: 0.8886 (mmm) cc_final: 0.8161 (mmm) REVERT: Q 192 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.4981 (t80) REVERT: Q 308 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6670 (t70) REVERT: Q 364 MET cc_start: 0.7396 (mmm) cc_final: 0.7041 (mmm) REVERT: Q 396 GLU cc_start: 0.8247 (tp30) cc_final: 0.7916 (tt0) REVERT: R 67 LYS cc_start: 0.8177 (mttt) cc_final: 0.7499 (mmtt) REVERT: R 88 MET cc_start: 0.7916 (mmm) cc_final: 0.7648 (mmm) REVERT: R 246 GLU cc_start: 0.4713 (OUTLIER) cc_final: 0.4414 (pp20) REVERT: R 364 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6974 (tm-30) REVERT: S 44 MET cc_start: 0.0292 (mtp) cc_final: -0.0508 (tpp) REVERT: S 190 MET cc_start: 0.2287 (tpp) cc_final: 0.1269 (mmm) REVERT: S 229 THR cc_start: 0.2623 (m) cc_final: 0.2197 (p) REVERT: S 354 GLN cc_start: 0.3965 (OUTLIER) cc_final: 0.2504 (tp40) REVERT: T 39 THR cc_start: 0.1519 (m) cc_final: 0.1035 (m) REVERT: U 227 MET cc_start: 0.1042 (mmt) cc_final: -0.0795 (ttp) REVERT: U 330 ILE cc_start: 0.0076 (OUTLIER) cc_final: -0.0535 (tt) REVERT: V 239 GLU cc_start: 0.3946 (OUTLIER) cc_final: 0.2728 (pt0) REVERT: W 128 MET cc_start: 0.3880 (ptm) cc_final: 0.2700 (mtm) REVERT: W 188 LYS cc_start: 0.1817 (tmtp) cc_final: 0.1103 (mmtm) outliers start: 202 outliers final: 116 residues processed: 662 average time/residue: 0.5240 time to fit residues: 592.5817 Evaluate side-chains 578 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 443 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 727 LEU Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 2067 GLN Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2087 LEU Chi-restraints excluded: chain I residue 2125 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 374 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 129 GLU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 355 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain N residue 407 THR Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 113 MET Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 216 ASP Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 351 LEU Chi-restraints excluded: chain P residue 375 CYS Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 431 SER Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain Q residue 323 ILE Chi-restraints excluded: chain Q residue 353 ASP Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 351 THR Chi-restraints excluded: chain S residue 354 GLN Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 327 HIS Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 272 CYS Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 214 LYS Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 229 GLN Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 271 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 611 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 361 optimal weight: 0.0870 chunk 462 optimal weight: 1.9990 chunk 358 optimal weight: 0.9980 chunk 533 optimal weight: 0.0010 chunk 353 optimal weight: 0.9990 chunk 631 optimal weight: 10.0000 chunk 395 optimal weight: 0.0670 chunk 384 optimal weight: 0.7980 chunk 291 optimal weight: 2.9990 overall best weight: 0.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 ASN ** M 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 369 GLN V 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5010 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 58334 Z= 0.162 Angle : 0.592 10.872 80061 Z= 0.304 Chirality : 0.041 0.356 9018 Planarity : 0.004 0.088 9229 Dihedral : 21.103 157.015 10376 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.32 % Favored : 94.47 % Rotamer: Outliers : 3.33 % Allowed : 19.99 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 6298 helix: 0.50 (0.10), residues: 2906 sheet: -0.22 (0.18), residues: 793 loop : -1.21 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP T 250 HIS 0.008 0.001 HIS M 316 PHE 0.028 0.001 PHE I 923 TYR 0.032 0.001 TYR K 17 ARG 0.009 0.000 ARG N 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 476 time to evaluate : 4.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 VAL cc_start: 0.7685 (t) cc_final: 0.7480 (t) REVERT: E 58 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7971 (mm) REVERT: E 92 GLU cc_start: 0.5127 (mt-10) cc_final: 0.4922 (mt-10) REVERT: F 59 MET cc_start: 0.8392 (mmp) cc_final: 0.8034 (mmt) REVERT: I 144 MET cc_start: -0.0635 (ppp) cc_final: -0.1685 (tmm) REVERT: I 895 MET cc_start: 0.7678 (tpp) cc_final: 0.7451 (tpt) REVERT: I 923 PHE cc_start: 0.6855 (p90) cc_final: 0.6576 (p90) REVERT: I 2036 ARG cc_start: 0.6877 (mmm160) cc_final: 0.6368 (mtm110) REVERT: I 2073 ASP cc_start: 0.6698 (t0) cc_final: 0.6490 (m-30) REVERT: J 187 LEU cc_start: 0.6399 (mt) cc_final: 0.6148 (mm) REVERT: K 1 MET cc_start: 0.2480 (OUTLIER) cc_final: 0.1774 (ppp) REVERT: K 64 TYR cc_start: 0.2035 (m-80) cc_final: 0.1546 (m-10) REVERT: K 138 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.6380 (p0) REVERT: K 196 MET cc_start: 0.5839 (tmm) cc_final: 0.5471 (tmm) REVERT: K 313 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.5742 (t80) REVERT: K 325 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6509 (mm) REVERT: M 242 ASP cc_start: 0.7150 (t0) cc_final: 0.6570 (m-30) REVERT: M 260 MET cc_start: 0.6303 (mpp) cc_final: 0.6053 (mpp) REVERT: M 268 LYS cc_start: 0.7424 (mttm) cc_final: 0.7020 (mmtp) REVERT: M 310 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6712 (pt0) REVERT: M 323 ILE cc_start: 0.8616 (pt) cc_final: 0.8339 (mt) REVERT: M 393 HIS cc_start: 0.7326 (t-90) cc_final: 0.7037 (t70) REVERT: M 402 THR cc_start: 0.8131 (m) cc_final: 0.7907 (p) REVERT: M 438 TYR cc_start: 0.8121 (m-80) cc_final: 0.7791 (m-80) REVERT: N 132 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8178 (mmtm) REVERT: N 168 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.7002 (ptp) REVERT: N 269 LYS cc_start: 0.7274 (pttt) cc_final: 0.6822 (ptpp) REVERT: N 326 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7906 (mtm) REVERT: N 354 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7888 (pp) REVERT: N 400 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.5785 (mtm180) REVERT: O 18 HIS cc_start: 0.6822 (OUTLIER) cc_final: 0.5384 (t-90) REVERT: O 223 LEU cc_start: 0.7337 (tp) cc_final: 0.6764 (tp) REVERT: O 265 LYS cc_start: 0.7024 (tptt) cc_final: 0.6720 (mmtt) REVERT: O 270 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: O 323 ILE cc_start: 0.8398 (pt) cc_final: 0.7924 (mt) REVERT: O 342 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: O 359 MET cc_start: 0.7641 (mtm) cc_final: 0.7286 (mtm) REVERT: O 423 ASP cc_start: 0.8562 (t0) cc_final: 0.8358 (t0) REVERT: P 46 MET cc_start: 0.8390 (tpp) cc_final: 0.8024 (mtp) REVERT: P 284 ARG cc_start: 0.6697 (ttt90) cc_final: 0.6308 (ttp-110) REVERT: P 349 ASP cc_start: 0.8072 (t0) cc_final: 0.7823 (t0) REVERT: P 448 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6628 (t0) REVERT: Q 61 MET cc_start: 0.8865 (mmm) cc_final: 0.8253 (mmm) REVERT: Q 173 ASP cc_start: 0.7038 (m-30) cc_final: 0.6541 (p0) REVERT: Q 192 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.5101 (t80) REVERT: Q 237 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7636 (p0) REVERT: Q 308 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6752 (t70) REVERT: Q 364 MET cc_start: 0.7367 (mmm) cc_final: 0.7023 (mmm) REVERT: Q 396 GLU cc_start: 0.8233 (tp30) cc_final: 0.7998 (tt0) REVERT: R 67 LYS cc_start: 0.8064 (mttt) cc_final: 0.7438 (mmtt) REVERT: R 88 MET cc_start: 0.7902 (mmm) cc_final: 0.7618 (mmm) REVERT: R 168 MET cc_start: 0.6442 (ptp) cc_final: 0.6033 (ptp) REVERT: R 246 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.4741 (pp20) REVERT: R 364 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6990 (tm-30) REVERT: S 44 MET cc_start: 0.0279 (mtp) cc_final: -0.0494 (tpp) REVERT: S 190 MET cc_start: 0.2316 (tpp) cc_final: 0.1331 (mmm) REVERT: S 229 THR cc_start: 0.2611 (m) cc_final: 0.2192 (p) REVERT: S 305 MET cc_start: 0.2289 (mmm) cc_final: 0.1807 (mmm) REVERT: S 354 GLN cc_start: 0.3900 (OUTLIER) cc_final: 0.2549 (tp40) REVERT: T 39 THR cc_start: 0.1245 (m) cc_final: 0.0569 (m) REVERT: T 376 MET cc_start: 0.0630 (mpp) cc_final: 0.0388 (tpp) REVERT: U 227 MET cc_start: 0.0994 (mmt) cc_final: -0.0812 (ttp) REVERT: U 330 ILE cc_start: 0.0576 (OUTLIER) cc_final: 0.0040 (tt) REVERT: V 239 GLU cc_start: 0.3578 (OUTLIER) cc_final: 0.2604 (pt0) REVERT: W 128 MET cc_start: 0.3887 (ptm) cc_final: 0.2727 (mtm) REVERT: W 188 LYS cc_start: 0.1741 (tmtp) cc_final: 0.1034 (mmtm) outliers start: 182 outliers final: 112 residues processed: 619 average time/residue: 0.5255 time to fit residues: 556.3635 Evaluate side-chains 582 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 448 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 722 ILE Chi-restraints excluded: chain I residue 727 LEU Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 974 LEU Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2125 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 304 ASN Chi-restraints excluded: chain K residue 313 PHE Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 374 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 310 GLU Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain N residue 407 THR Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 216 ASP Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 351 LEU Chi-restraints excluded: chain P residue 375 CYS Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 431 SER Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 237 ASP Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain Q residue 353 ASP Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 267 GLU Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain S residue 274 ILE Chi-restraints excluded: chain S residue 351 THR Chi-restraints excluded: chain S residue 354 GLN Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 327 HIS Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 272 CYS Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 390 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 124 optimal weight: 0.0770 chunk 122 optimal weight: 0.0070 chunk 401 optimal weight: 0.6980 chunk 430 optimal weight: 4.9990 chunk 312 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 496 optimal weight: 0.8980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN I 865 GLN K 44 GLN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 387 HIS ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 393 HIS V 113 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5003 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 58334 Z= 0.159 Angle : 0.584 10.369 80061 Z= 0.298 Chirality : 0.041 0.394 9018 Planarity : 0.004 0.092 9229 Dihedral : 20.961 156.361 10372 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.19 % Favored : 94.60 % Rotamer: Outliers : 3.00 % Allowed : 20.08 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.11), residues: 6298 helix: 0.66 (0.10), residues: 2898 sheet: -0.26 (0.18), residues: 818 loop : -1.14 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 277 HIS 0.009 0.001 HIS M 316 PHE 0.025 0.001 PHE I 923 TYR 0.035 0.001 TYR K 17 ARG 0.009 0.000 ARG N 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 468 time to evaluate : 4.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 VAL cc_start: 0.7753 (t) cc_final: 0.7537 (t) REVERT: E 58 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7995 (mm) REVERT: F 59 MET cc_start: 0.8434 (mmp) cc_final: 0.8195 (mmt) REVERT: I 144 MET cc_start: -0.0658 (ppp) cc_final: -0.1651 (tmm) REVERT: I 198 MET cc_start: 0.3625 (ptt) cc_final: 0.3297 (ptt) REVERT: I 860 ARG cc_start: 0.6751 (ttp-110) cc_final: 0.6352 (ttp80) REVERT: I 895 MET cc_start: 0.7687 (tpp) cc_final: 0.7456 (tpt) REVERT: I 923 PHE cc_start: 0.6963 (p90) cc_final: 0.6658 (p90) REVERT: I 2036 ARG cc_start: 0.6855 (mmm160) cc_final: 0.6356 (mtm110) REVERT: I 2073 ASP cc_start: 0.6715 (t0) cc_final: 0.6501 (m-30) REVERT: J 187 LEU cc_start: 0.6260 (mt) cc_final: 0.5984 (mm) REVERT: K 1 MET cc_start: 0.2244 (OUTLIER) cc_final: 0.1583 (ppp) REVERT: K 64 TYR cc_start: 0.1560 (m-80) cc_final: 0.1257 (m-10) REVERT: K 255 MET cc_start: 0.0284 (mmp) cc_final: -0.0711 (mmm) REVERT: K 314 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.5118 (p90) REVERT: K 325 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6502 (mm) REVERT: M 163 THR cc_start: 0.8853 (p) cc_final: 0.8487 (t) REVERT: M 242 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: M 268 LYS cc_start: 0.7410 (mttm) cc_final: 0.7033 (mmtp) REVERT: M 308 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6229 (m-30) REVERT: M 310 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6746 (pt0) REVERT: M 323 ILE cc_start: 0.8601 (pt) cc_final: 0.8350 (mt) REVERT: M 402 THR cc_start: 0.8170 (m) cc_final: 0.7950 (p) REVERT: M 438 TYR cc_start: 0.8102 (m-80) cc_final: 0.7790 (m-80) REVERT: N 46 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8008 (mmm) REVERT: N 132 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8156 (mmtm) REVERT: N 168 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.7009 (ptp) REVERT: N 269 LYS cc_start: 0.7277 (pttt) cc_final: 0.6830 (ptpp) REVERT: N 326 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8077 (mtm) REVERT: N 354 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7891 (pp) REVERT: N 400 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5733 (mtm180) REVERT: O 18 HIS cc_start: 0.6755 (OUTLIER) cc_final: 0.5530 (t-90) REVERT: O 223 LEU cc_start: 0.7286 (tp) cc_final: 0.6707 (tp) REVERT: O 259 MET cc_start: 0.6876 (ttt) cc_final: 0.6544 (ttt) REVERT: O 270 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: O 323 ILE cc_start: 0.8421 (pt) cc_final: 0.7975 (mt) REVERT: O 342 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: O 359 MET cc_start: 0.7506 (mtm) cc_final: 0.7149 (mtm) REVERT: O 423 ASP cc_start: 0.8558 (t0) cc_final: 0.8343 (t0) REVERT: P 19 ILE cc_start: 0.5326 (mt) cc_final: 0.5096 (mm) REVERT: P 46 MET cc_start: 0.8255 (tpp) cc_final: 0.7911 (mtp) REVERT: P 284 ARG cc_start: 0.6710 (ttt90) cc_final: 0.6320 (ttp-110) REVERT: P 349 ASP cc_start: 0.8078 (t0) cc_final: 0.7859 (t0) REVERT: P 448 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6521 (t0) REVERT: Q 61 MET cc_start: 0.8858 (mmm) cc_final: 0.8188 (mmm) REVERT: Q 173 ASP cc_start: 0.7046 (m-30) cc_final: 0.6576 (p0) REVERT: Q 237 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7631 (p0) REVERT: Q 308 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6787 (t70) REVERT: Q 364 MET cc_start: 0.7452 (mmm) cc_final: 0.7130 (mmm) REVERT: Q 396 GLU cc_start: 0.8229 (tp30) cc_final: 0.7959 (tt0) REVERT: R 67 LYS cc_start: 0.8065 (mttt) cc_final: 0.7500 (mmtt) REVERT: R 88 MET cc_start: 0.7890 (mmm) cc_final: 0.7636 (mmt) REVERT: R 168 MET cc_start: 0.6346 (ptp) cc_final: 0.5995 (ptp) REVERT: R 246 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.5093 (pp20) REVERT: R 364 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6977 (tm-30) REVERT: S 44 MET cc_start: 0.0266 (mtp) cc_final: -0.0496 (tpp) REVERT: S 190 MET cc_start: 0.2030 (tpp) cc_final: 0.1115 (mmm) REVERT: S 229 THR cc_start: 0.2363 (m) cc_final: 0.1968 (p) REVERT: S 305 MET cc_start: 0.2795 (mmm) cc_final: 0.2130 (mmm) REVERT: S 354 GLN cc_start: 0.3849 (OUTLIER) cc_final: 0.2526 (tp40) REVERT: T 39 THR cc_start: 0.1607 (m) cc_final: 0.0932 (m) REVERT: T 376 MET cc_start: 0.0612 (mpp) cc_final: 0.0401 (tpp) REVERT: U 227 MET cc_start: 0.0965 (mmt) cc_final: -0.0827 (ttp) REVERT: U 330 ILE cc_start: 0.0205 (OUTLIER) cc_final: -0.0031 (tt) REVERT: V 239 GLU cc_start: 0.4725 (OUTLIER) cc_final: 0.3484 (pt0) REVERT: W 128 MET cc_start: 0.3914 (ptm) cc_final: 0.2775 (mtm) REVERT: W 188 LYS cc_start: 0.1728 (tmtp) cc_final: 0.1029 (mmtm) outliers start: 164 outliers final: 110 residues processed: 602 average time/residue: 0.5274 time to fit residues: 540.7242 Evaluate side-chains 572 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 439 time to evaluate : 4.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 650 THR Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 722 ILE Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 774 THR Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 856 VAL Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2125 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 304 ASN Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 242 ASP Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 310 GLU Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 355 LEU Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain N residue 407 THR Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 216 ASP Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 375 CYS Chi-restraints excluded: chain P residue 431 SER Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 237 ASP Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain Q residue 353 ASP Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain S residue 274 ILE Chi-restraints excluded: chain S residue 351 THR Chi-restraints excluded: chain S residue 354 GLN Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 327 HIS Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 272 CYS Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 271 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 574 optimal weight: 8.9990 chunk 604 optimal weight: 0.8980 chunk 551 optimal weight: 7.9990 chunk 588 optimal weight: 8.9990 chunk 354 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 461 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 531 optimal weight: 9.9990 chunk 556 optimal weight: 0.0000 chunk 586 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN K 110 ASN ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 226 GLN ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5068 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 58334 Z= 0.280 Angle : 0.648 13.246 80061 Z= 0.330 Chirality : 0.043 0.376 9018 Planarity : 0.005 0.080 9229 Dihedral : 21.014 153.652 10367 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.65 % Favored : 94.16 % Rotamer: Outliers : 3.05 % Allowed : 20.37 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 6298 helix: 0.53 (0.10), residues: 2897 sheet: -0.27 (0.18), residues: 814 loop : -1.15 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 806 HIS 0.008 0.001 HIS M 316 PHE 0.025 0.002 PHE I 923 TYR 0.033 0.002 TYR K 17 ARG 0.016 0.001 ARG L 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 447 time to evaluate : 4.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 VAL cc_start: 0.7851 (t) cc_final: 0.7635 (t) REVERT: E 58 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8038 (mm) REVERT: F 59 MET cc_start: 0.8577 (mmp) cc_final: 0.8357 (mmt) REVERT: I 198 MET cc_start: 0.3531 (ptt) cc_final: 0.3122 (ptt) REVERT: I 895 MET cc_start: 0.7650 (tpp) cc_final: 0.7401 (tpt) REVERT: I 2026 CYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7308 (t) REVERT: I 2036 ARG cc_start: 0.6848 (mmm160) cc_final: 0.6380 (mtm110) REVERT: I 2073 ASP cc_start: 0.6762 (t0) cc_final: 0.6553 (m-30) REVERT: J 146 LEU cc_start: 0.7930 (tp) cc_final: 0.7640 (mp) REVERT: J 187 LEU cc_start: 0.6460 (mt) cc_final: 0.6234 (mm) REVERT: J 189 THR cc_start: 0.4707 (p) cc_final: 0.4485 (p) REVERT: K 1 MET cc_start: 0.2461 (OUTLIER) cc_final: 0.1783 (ppp) REVERT: K 64 TYR cc_start: 0.1988 (m-80) cc_final: 0.1733 (m-10) REVERT: K 196 MET cc_start: 0.5948 (tmm) cc_final: 0.5383 (tmm) REVERT: K 255 MET cc_start: -0.0165 (mmp) cc_final: -0.1155 (mmm) REVERT: K 313 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.5874 (t80) REVERT: K 314 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.5327 (p90) REVERT: K 375 MET cc_start: 0.5310 (tpt) cc_final: 0.5003 (tpt) REVERT: M 163 THR cc_start: 0.8785 (p) cc_final: 0.8513 (t) REVERT: M 242 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6694 (m-30) REVERT: M 268 LYS cc_start: 0.7503 (mttm) cc_final: 0.7178 (mmtp) REVERT: M 310 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6767 (pt0) REVERT: M 323 ILE cc_start: 0.8528 (pt) cc_final: 0.8196 (mt) REVERT: N 132 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8129 (mmtm) REVERT: N 269 LYS cc_start: 0.7419 (pttt) cc_final: 0.6887 (ptpp) REVERT: N 354 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8037 (pp) REVERT: N 400 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.5832 (mtm-85) REVERT: O 18 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.5542 (t-90) REVERT: O 259 MET cc_start: 0.7093 (ttt) cc_final: 0.6714 (ttt) REVERT: O 270 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: O 323 ILE cc_start: 0.8449 (pt) cc_final: 0.7983 (mt) REVERT: O 342 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: O 359 MET cc_start: 0.7786 (mtm) cc_final: 0.7364 (mtm) REVERT: P 19 ILE cc_start: 0.5498 (mt) cc_final: 0.4902 (tt) REVERT: P 284 ARG cc_start: 0.6671 (ttt90) cc_final: 0.6327 (ttp-110) REVERT: P 349 ASP cc_start: 0.8081 (t0) cc_final: 0.7806 (t0) REVERT: P 448 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.6944 (t0) REVERT: Q 61 MET cc_start: 0.8873 (mmm) cc_final: 0.8175 (mmm) REVERT: Q 173 ASP cc_start: 0.7277 (m-30) cc_final: 0.6784 (p0) REVERT: Q 192 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.5186 (t80) REVERT: Q 237 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7865 (p0) REVERT: Q 308 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6778 (t70) REVERT: Q 364 MET cc_start: 0.7464 (mmm) cc_final: 0.7104 (mmm) REVERT: Q 396 GLU cc_start: 0.8271 (tp30) cc_final: 0.7937 (tt0) REVERT: R 67 LYS cc_start: 0.8044 (mttt) cc_final: 0.7405 (mmtt) REVERT: R 88 MET cc_start: 0.7919 (mmm) cc_final: 0.7650 (mmt) REVERT: R 131 ILE cc_start: 0.6265 (mt) cc_final: 0.6041 (pt) REVERT: R 246 GLU cc_start: 0.5026 (OUTLIER) cc_final: 0.4741 (pp20) REVERT: R 364 GLU cc_start: 0.7308 (tm-30) cc_final: 0.7021 (tm-30) REVERT: S 44 MET cc_start: 0.0134 (mtp) cc_final: -0.0578 (tpp) REVERT: S 229 THR cc_start: 0.2646 (m) cc_final: 0.2204 (p) REVERT: S 305 MET cc_start: 0.2551 (mmm) cc_final: 0.1925 (mmm) REVERT: S 354 GLN cc_start: 0.4057 (OUTLIER) cc_final: 0.2740 (tp40) REVERT: T 39 THR cc_start: 0.1655 (m) cc_final: 0.0951 (m) REVERT: U 227 MET cc_start: 0.0924 (mmt) cc_final: -0.0841 (ttp) REVERT: U 330 ILE cc_start: 0.0231 (OUTLIER) cc_final: 0.0005 (tt) REVERT: V 90 LYS cc_start: 0.3123 (OUTLIER) cc_final: 0.2240 (mmtp) REVERT: V 239 GLU cc_start: 0.4429 (OUTLIER) cc_final: 0.3442 (pt0) REVERT: W 128 MET cc_start: 0.4209 (ptm) cc_final: 0.3220 (mtm) outliers start: 167 outliers final: 123 residues processed: 577 average time/residue: 0.5194 time to fit residues: 511.9291 Evaluate side-chains 580 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 435 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 650 THR Chi-restraints excluded: chain I residue 703 LYS Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 722 ILE Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 774 THR Chi-restraints excluded: chain I residue 856 VAL Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 900 VAL Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 974 LEU Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2034 ASP Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2087 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 313 PHE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 242 ASP Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 310 GLU Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 355 LEU Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain N residue 407 THR Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 257 LEU Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 216 ASP Chi-restraints excluded: chain P residue 226 GLN Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 375 CYS Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain P residue 431 SER Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 237 ASP Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain Q residue 353 ASP Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 90 MET Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain S residue 274 ILE Chi-restraints excluded: chain S residue 351 THR Chi-restraints excluded: chain S residue 354 GLN Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 272 CYS Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 90 LYS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 386 optimal weight: 0.3980 chunk 622 optimal weight: 3.9990 chunk 379 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 432 optimal weight: 0.9990 chunk 652 optimal weight: 10.0000 chunk 600 optimal weight: 0.9980 chunk 519 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 401 optimal weight: 0.6980 chunk 318 optimal weight: 0.0370 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 ASN ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5061 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 58334 Z= 0.250 Angle : 0.698 59.200 80061 Z= 0.367 Chirality : 0.043 0.512 9018 Planarity : 0.005 0.084 9229 Dihedral : 21.009 153.734 10366 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.64 % Favored : 94.17 % Rotamer: Outliers : 2.98 % Allowed : 20.48 % Favored : 76.54 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 6298 helix: 0.54 (0.10), residues: 2898 sheet: -0.28 (0.18), residues: 814 loop : -1.14 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 277 HIS 0.009 0.001 HIS M 316 PHE 0.042 0.002 PHE K 216 TYR 0.032 0.001 TYR K 17 ARG 0.012 0.000 ARG C 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 435 time to evaluate : 4.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 VAL cc_start: 0.7848 (t) cc_final: 0.7629 (t) REVERT: E 58 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8032 (mm) REVERT: F 59 MET cc_start: 0.8572 (mmp) cc_final: 0.8354 (mmt) REVERT: I 895 MET cc_start: 0.7636 (tpp) cc_final: 0.7389 (tpt) REVERT: I 2036 ARG cc_start: 0.6847 (mmm160) cc_final: 0.6394 (mtm110) REVERT: I 2073 ASP cc_start: 0.6760 (t0) cc_final: 0.6552 (m-30) REVERT: J 146 LEU cc_start: 0.7920 (tp) cc_final: 0.7639 (mp) REVERT: J 187 LEU cc_start: 0.6451 (mt) cc_final: 0.6226 (mm) REVERT: J 189 THR cc_start: 0.4701 (p) cc_final: 0.4480 (p) REVERT: K 1 MET cc_start: 0.2456 (OUTLIER) cc_final: 0.1784 (ppp) REVERT: K 64 TYR cc_start: 0.1982 (m-80) cc_final: 0.1727 (m-10) REVERT: K 196 MET cc_start: 0.5954 (tmm) cc_final: 0.5386 (tmm) REVERT: K 255 MET cc_start: -0.0166 (mmp) cc_final: -0.1140 (mmm) REVERT: K 313 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.5820 (t80) REVERT: K 314 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.5312 (p90) REVERT: K 325 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6677 (mm) REVERT: K 375 MET cc_start: 0.5400 (tpt) cc_final: 0.5067 (tpt) REVERT: M 163 THR cc_start: 0.8785 (p) cc_final: 0.8505 (t) REVERT: M 242 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6683 (m-30) REVERT: M 260 MET cc_start: 0.6751 (mpp) cc_final: 0.6518 (mpp) REVERT: M 268 LYS cc_start: 0.7496 (mttm) cc_final: 0.7169 (mmtp) REVERT: M 310 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6754 (pt0) REVERT: M 323 ILE cc_start: 0.8522 (pt) cc_final: 0.8195 (mt) REVERT: N 132 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8124 (mmtm) REVERT: N 269 LYS cc_start: 0.7402 (pttt) cc_final: 0.6876 (ptpp) REVERT: N 354 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8030 (pp) REVERT: N 400 ARG cc_start: 0.6368 (OUTLIER) cc_final: 0.5896 (mtm180) REVERT: O 18 HIS cc_start: 0.6963 (OUTLIER) cc_final: 0.5541 (t-90) REVERT: O 259 MET cc_start: 0.7030 (ttt) cc_final: 0.6649 (ttt) REVERT: O 270 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: O 323 ILE cc_start: 0.8440 (pt) cc_final: 0.7981 (mt) REVERT: O 342 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: O 359 MET cc_start: 0.7789 (mtm) cc_final: 0.7360 (mtm) REVERT: P 19 ILE cc_start: 0.5488 (mt) cc_final: 0.4893 (tt) REVERT: P 284 ARG cc_start: 0.6668 (ttt90) cc_final: 0.6321 (ttp-110) REVERT: P 349 ASP cc_start: 0.8073 (t0) cc_final: 0.7796 (t0) REVERT: P 448 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.6924 (t0) REVERT: Q 61 MET cc_start: 0.8867 (mmm) cc_final: 0.8164 (mmm) REVERT: Q 173 ASP cc_start: 0.7268 (m-30) cc_final: 0.6779 (p0) REVERT: Q 192 TYR cc_start: 0.6695 (OUTLIER) cc_final: 0.5182 (t80) REVERT: Q 237 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7855 (p0) REVERT: Q 364 MET cc_start: 0.7458 (mmm) cc_final: 0.7100 (mmm) REVERT: Q 396 GLU cc_start: 0.8269 (tp30) cc_final: 0.7935 (tt0) REVERT: R 67 LYS cc_start: 0.8038 (mttt) cc_final: 0.7397 (mmtt) REVERT: R 88 MET cc_start: 0.7919 (mmm) cc_final: 0.7648 (mmt) REVERT: R 131 ILE cc_start: 0.6247 (mt) cc_final: 0.6036 (pt) REVERT: R 246 GLU cc_start: 0.5225 (OUTLIER) cc_final: 0.4892 (pp20) REVERT: R 364 GLU cc_start: 0.7304 (tm-30) cc_final: 0.7011 (tm-30) REVERT: S 44 MET cc_start: 0.0134 (mtp) cc_final: -0.0578 (tpp) REVERT: S 229 THR cc_start: 0.2639 (m) cc_final: 0.2205 (p) REVERT: S 305 MET cc_start: 0.2545 (mmm) cc_final: 0.1924 (mmm) REVERT: S 354 GLN cc_start: 0.3904 (OUTLIER) cc_final: 0.2547 (tp40) REVERT: T 39 THR cc_start: 0.1640 (m) cc_final: 0.0947 (m) REVERT: U 227 MET cc_start: 0.0931 (mmt) cc_final: -0.0841 (ttp) REVERT: U 330 ILE cc_start: 0.0235 (OUTLIER) cc_final: 0.0005 (tt) REVERT: V 90 LYS cc_start: 0.3118 (OUTLIER) cc_final: 0.2289 (mmtp) REVERT: V 239 GLU cc_start: 0.4429 (OUTLIER) cc_final: 0.3439 (pt0) REVERT: W 128 MET cc_start: 0.4206 (ptm) cc_final: 0.3216 (mtm) outliers start: 163 outliers final: 130 residues processed: 560 average time/residue: 0.5268 time to fit residues: 503.3481 Evaluate side-chains 584 residues out of total 5487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 433 time to evaluate : 4.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 650 THR Chi-restraints excluded: chain I residue 703 LYS Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 722 ILE Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 774 THR Chi-restraints excluded: chain I residue 814 MET Chi-restraints excluded: chain I residue 833 LEU Chi-restraints excluded: chain I residue 856 VAL Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 974 LEU Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 1989 SER Chi-restraints excluded: chain I residue 2034 ASP Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2087 LEU Chi-restraints excluded: chain I residue 2196 PHE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 304 ASN Chi-restraints excluded: chain K residue 313 PHE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 333 VAL Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 242 ASP Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 310 GLU Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 355 LEU Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain N residue 407 THR Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 257 LEU Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 216 ASP Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 375 CYS Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain P residue 431 SER Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 237 ASP Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 353 ASP Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain S residue 274 ILE Chi-restraints excluded: chain S residue 351 THR Chi-restraints excluded: chain S residue 354 GLN Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 160 THR Chi-restraints excluded: chain U residue 165 ILE Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 272 CYS Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 90 LYS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 217 VAL Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 245 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 412 optimal weight: 0.5980 chunk 553 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 479 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 520 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 chunk 534 optimal weight: 0.0870 chunk 65 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 ASN ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.168012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.134239 restraints weight = 122731.320| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.79 r_work: 0.3537 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 58334 Z= 0.250 Angle : 0.698 59.200 80061 Z= 0.367 Chirality : 0.043 0.512 9018 Planarity : 0.005 0.089 9229 Dihedral : 21.008 153.734 10364 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.64 % Favored : 94.17 % Rotamer: Outliers : 2.76 % Allowed : 20.57 % Favored : 76.66 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 6298 helix: 0.54 (0.10), residues: 2898 sheet: -0.28 (0.18), residues: 814 loop : -1.14 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 277 HIS 0.009 0.001 HIS M 316 PHE 0.042 0.002 PHE K 216 TYR 0.032 0.001 TYR K 17 ARG 0.012 0.000 ARG C 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12424.96 seconds wall clock time: 218 minutes 48.42 seconds (13128.42 seconds total)