Starting phenix.real_space_refine on Sun Feb 25 16:17:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nav_12249/02_2024/7nav_12249_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nav_12249/02_2024/7nav_12249.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nav_12249/02_2024/7nav_12249_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nav_12249/02_2024/7nav_12249_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nav_12249/02_2024/7nav_12249_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nav_12249/02_2024/7nav_12249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nav_12249/02_2024/7nav_12249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nav_12249/02_2024/7nav_12249_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nav_12249/02_2024/7nav_12249_neut_updated.pdb" } resolution = 4.8 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= 0.005 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1510 5.49 5 Mg 37 5.21 5 S 78 5.16 5 C 27231 2.51 5 N 9818 2.21 5 O 14168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 52843 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 32412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1510, 32412 Classifications: {'RNA': 1510} Modifications used: {'rna2p_pur': 113, 'rna2p_pyr': 89, 'rna3p': 8, 'rna3p_pur': 742, 'rna3p_pyr': 558} Link IDs: {'rna2p': 202, 'rna3p': 1307} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "S" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "V" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Unusual residues: {' MG': 37} Classifications: {'undetermined': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.21, per 1000 atoms: 0.50 Number of scatterers: 52843 At special positions: 0 Unit cell: (145.39, 240.87, 196.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 78 16.00 P 1510 15.00 Mg 37 11.99 O 14168 8.00 N 9818 7.00 C 27231 6.00 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: 38.58 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4810 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 24 sheets defined 38.2% alpha, 13.9% beta 425 base pairs and 738 stacking pairs defined. Time for finding SS restraints: 30.05 Creating SS restraints... Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 43 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.674A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 95 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.899A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 50 through 64 Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 147 through 150 No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 153 through 160 removed outlier: 4.816A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.660A pdb=" N ALA E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 143 Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'F' and resid 18 through 31 removed outlier: 3.734A pdb=" N ILE F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 removed outlier: 4.046A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 105 removed outlier: 3.748A pdb=" N ALA F 105 " --> pdb=" O PRO F 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 101 through 105' Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 36 through 53 removed outlier: 3.573A pdb=" N ALA G 46 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 removed outlier: 4.284A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 111 Processing helix chain 'G' and resid 116 through 129 removed outlier: 3.516A pdb=" N SER G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 147 removed outlier: 3.613A pdb=" N ALA G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU G 146 " --> pdb=" O HIS G 142 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA G 147 " --> pdb=" O ARG G 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 20 Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 55 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 72 through 91 Processing helix chain 'I' and resid 95 through 101 Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 through 88 removed outlier: 4.240A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 55 through 58 No H-bonds generated for 'chain 'K' and resid 55 through 58' Processing helix chain 'K' and resid 60 through 77 removed outlier: 4.036A pdb=" N ALA K 67 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 103 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 117 Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 62 removed outlier: 4.582A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 82 removed outlier: 4.404A pdb=" N LEU M 80 " --> pdb=" O SER M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 92 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 19 Processing helix chain 'N' and resid 21 through 32 Processing helix chain 'N' and resid 40 through 50 Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.897A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 15 removed outlier: 3.543A pdb=" N GLU O 14 " --> pdb=" O LYS O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 45 removed outlier: 3.668A pdb=" N LEU O 31 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 71 removed outlier: 3.872A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN O 62 " --> pdb=" O ARG O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 Processing helix chain 'P' and resid 54 through 63 Processing helix chain 'P' and resid 69 through 81 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 13 through 16 No H-bonds generated for 'chain 'R' and resid 13 through 16' Processing helix chain 'R' and resid 26 through 31 Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'S' and resid 13 through 25 Processing helix chain 'T' and resid 5 through 41 removed outlier: 3.665A pdb=" N LYS T 9 " --> pdb=" O LYS T 5 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG T 10 " --> pdb=" O SER T 6 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG T 24 " --> pdb=" O HIS T 20 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 63 Proline residue: T 56 - end of helix removed outlier: 3.513A pdb=" N ASP T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 86 Processing helix chain 'V' and resid 8 through 25 removed outlier: 4.707A pdb=" N GLN V 13 " --> pdb=" O GLN V 9 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU V 14 " --> pdb=" O ARG V 10 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS V 17 " --> pdb=" O GLN V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 47 No H-bonds generated for 'chain 'V' and resid 45 through 47' Processing helix chain 'V' and resid 62 through 74 removed outlier: 3.654A pdb=" N ALA V 67 " --> pdb=" O ASP V 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY V 68 " --> pdb=" O ALA V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 85 Processing helix chain 'X' and resid 5 through 19 removed outlier: 4.130A pdb=" N ALA X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 48 through 65 removed outlier: 4.234A pdb=" N VAL X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU X 65 " --> pdb=" O VAL X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 93 Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.696A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.928A pdb=" N ILE B 40 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 54 through 58 Processing sheet with id= D, first strand: chain 'C' and resid 165 through 171 Processing sheet with id= E, first strand: chain 'D' and resid 123 through 125 Processing sheet with id= F, first strand: chain 'E' and resid 47 through 53 removed outlier: 3.548A pdb=" N THR E 37 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 85 through 88 Processing sheet with id= H, first strand: chain 'F' and resid 2 through 10 removed outlier: 3.644A pdb=" N VAL F 10 " --> pdb=" O HIS F 58 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 35 through 41 removed outlier: 3.544A pdb=" N LYS F 35 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 73 through 75 Processing sheet with id= K, first strand: chain 'H' and resid 110 through 112 removed outlier: 5.677A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 5 through 11 Processing sheet with id= M, first strand: chain 'I' and resid 21 through 23 Processing sheet with id= N, first strand: chain 'J' and resid 70 through 76 Processing sheet with id= O, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= P, first strand: chain 'K' and resid 20 through 24 removed outlier: 4.348A pdb=" N VAL K 20 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE K 31 " --> pdb=" O HIS K 24 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 83 through 86 removed outlier: 6.796A pdb=" N ASN K 109 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL K 86 " --> pdb=" O ASN K 109 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR K 111 " --> pdb=" O VAL K 86 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'L' and resid 95 through 98 removed outlier: 4.874A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE L 82 " --> pdb=" O LYS L 30 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS L 30 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'P' and resid 3 through 5 removed outlier: 6.731A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Q' and resid 58 through 62 removed outlier: 16.048A pdb=" N THR Q 7 " --> pdb=" O PHE Q 28 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N PHE Q 28 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S' and resid 31 through 33 removed outlier: 4.056A pdb=" N LEU S 31 " --> pdb=" O THR S 48 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'V' and resid 94 through 98 removed outlier: 6.180A pdb=" N THR V 55 " --> pdb=" O VAL V 38 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL V 38 " --> pdb=" O THR V 55 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 75 through 77 removed outlier: 6.134A pdb=" N ASP X 41 " --> pdb=" O LEU X 23 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU X 23 " --> pdb=" O ASP X 41 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 143 through 146 removed outlier: 6.894A pdb=" N THR X 126 " --> pdb=" O LYS X 118 " (cutoff:3.500A) 795 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 954 hydrogen bonds 1118 hydrogen bond angles 0 basepair planarities 425 basepair parallelities 738 stacking parallelities Total time for adding SS restraints: 40.36 Time building geometry restraints manager: 39.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8085 1.33 - 1.45: 22783 1.45 - 1.57: 22953 1.57 - 1.70: 3016 1.70 - 1.82: 141 Bond restraints: 56978 Sorted by residual: bond pdb=" O3' U A 571 " pdb=" P A A 572 " ideal model delta sigma weight residual 1.607 1.469 0.138 1.50e-02 4.44e+03 8.44e+01 bond pdb=" N3 2MG A1207 " pdb=" C4 2MG A1207 " ideal model delta sigma weight residual 1.496 1.342 0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.313 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.347 0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" N3 2MG A 966 " pdb=" C4 2MG A 966 " ideal model delta sigma weight residual 1.496 1.353 0.143 2.00e-02 2.50e+03 5.09e+01 ... (remaining 56973 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.94: 8309 105.94 - 113.95: 36348 113.95 - 121.96: 27421 121.96 - 129.97: 11352 129.97 - 137.98: 970 Bond angle restraints: 84400 Sorted by residual: angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 129.37 -34.41 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C ILE V 91 " pdb=" N VAL V 92 " pdb=" CA VAL V 92 " ideal model delta sigma weight residual 122.60 117.86 4.74 6.80e-01 2.16e+00 4.87e+01 angle pdb=" C LYS H 56 " pdb=" CA LYS H 56 " pdb=" CB LYS H 56 " ideal model delta sigma weight residual 111.00 116.99 -5.99 8.70e-01 1.32e+00 4.75e+01 angle pdb=" N SER I 93 " pdb=" CA SER I 93 " pdb=" C SER I 93 " ideal model delta sigma weight residual 113.88 105.95 7.93 1.23e+00 6.61e-01 4.16e+01 angle pdb=" CA PRO V 30 " pdb=" N PRO V 30 " pdb=" CD PRO V 30 " ideal model delta sigma weight residual 112.00 103.41 8.59 1.40e+00 5.10e-01 3.77e+01 ... (remaining 84395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 31695 35.79 - 71.57: 4176 71.57 - 107.36: 494 107.36 - 143.15: 15 143.15 - 178.93: 9 Dihedral angle restraints: 36389 sinusoidal: 28949 harmonic: 7440 Sorted by residual: dihedral pdb=" O4' U A1008 " pdb=" C1' U A1008 " pdb=" N1 U A1008 " pdb=" C2 U A1008 " ideal model delta sinusoidal sigma weight residual 200.00 33.90 166.10 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 46.50 153.50 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 51.17 148.83 1 1.50e+01 4.44e-03 7.92e+01 ... (remaining 36386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 9191 0.083 - 0.165: 1162 0.165 - 0.248: 263 0.248 - 0.330: 28 0.330 - 0.413: 7 Chirality restraints: 10651 Sorted by residual: chirality pdb=" CA ASN D 89 " pdb=" N ASN D 89 " pdb=" C ASN D 89 " pdb=" CB ASN D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ASN T 52 " pdb=" N ASN T 52 " pdb=" C ASN T 52 " pdb=" CB ASN T 52 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C3' C A1103 " pdb=" C4' C A1103 " pdb=" O3' C A1103 " pdb=" C2' C A1103 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 10648 not shown) Planarity restraints: 5111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.060 2.00e-02 2.50e+03 6.06e-01 8.25e+03 pdb=" C4' 2MG A1207 " -0.456 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.652 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.644 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.178 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.967 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.218 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.943 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.060 2.00e-02 2.50e+03 5.85e-01 7.69e+03 pdb=" C4' 2MG A1516 " 0.432 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.571 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.632 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.171 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.979 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.230 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.877 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A 966 " -0.244 2.00e-02 2.50e+03 4.30e-01 4.16e+03 pdb=" C4' 2MG A 966 " 0.408 2.00e-02 2.50e+03 pdb=" O4' 2MG A 966 " 0.603 2.00e-02 2.50e+03 pdb=" C3' 2MG A 966 " -0.481 2.00e-02 2.50e+03 pdb=" O3' 2MG A 966 " -0.131 2.00e-02 2.50e+03 pdb=" C2' 2MG A 966 " -0.346 2.00e-02 2.50e+03 pdb=" O2' 2MG A 966 " 0.478 2.00e-02 2.50e+03 pdb=" C1' 2MG A 966 " 0.324 2.00e-02 2.50e+03 pdb=" N9 2MG A 966 " -0.610 2.00e-02 2.50e+03 ... (remaining 5108 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.83: 10 1.83 - 2.60: 2135 2.60 - 3.37: 83298 3.37 - 4.13: 187470 4.13 - 4.90: 253569 Nonbonded interactions: 526482 Sorted by model distance: nonbonded pdb=" C2' G A1387 " pdb="MG MG A1630 " model vdw 1.065 2.600 nonbonded pdb=" C3' G A1387 " pdb="MG MG A1630 " model vdw 1.068 2.600 nonbonded pdb=" O3' G A1387 " pdb="MG MG A1630 " model vdw 1.429 2.170 nonbonded pdb=" O3' U A 952 " pdb="MG MG A1633 " model vdw 1.519 2.170 nonbonded pdb=" OP1 A A1197 " pdb="MG MG A1635 " model vdw 1.629 2.170 ... (remaining 526477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.220 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: 0.050 Extract box with map and model: 14.830 Check model and map are aligned: 0.700 Set scattering table: 0.480 Process input model: 194.800 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.150 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 217.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.009 0.154 56978 Z= 0.576 Angle : 1.024 34.408 84400 Z= 0.638 Chirality : 0.061 0.413 10651 Planarity : 0.016 0.606 5111 Dihedral : 24.374 178.933 31579 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 43.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % 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: -2.28 (0.15), residues: 2550 helix: -1.00 (0.16), residues: 975 sheet: -1.54 (0.24), residues: 409 loop : -1.87 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 42 HIS 0.011 0.002 HIS Q 47 PHE 0.023 0.002 PHE X 94 TYR 0.016 0.002 TYR L 95 ARG 0.034 0.001 ARG V 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 618 time to evaluate : 3.329 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: 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: 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: B 24 ASN cc_start: 0.6981 (t0) cc_final: 0.6562 (t0) REVERT: B 89 GLN cc_start: 0.6922 (mm-40) cc_final: 0.6716 (mm-40) REVERT: B 90 PHE cc_start: 0.7334 (m-80) cc_final: 0.7058 (m-80) REVERT: B 115 LYS cc_start: 0.8631 (mttt) cc_final: 0.8381 (mtmt) REVERT: B 144 LEU cc_start: 0.9269 (mt) cc_final: 0.8733 (mp) REVERT: B 189 THR cc_start: 0.3952 (p) cc_final: 0.3609 (p) REVERT: C 37 PHE cc_start: 0.8528 (t80) cc_final: 0.8088 (t80) REVERT: C 134 MET cc_start: 0.8749 (ptp) cc_final: 0.8490 (ptp) REVERT: C 181 ASP cc_start: 0.8701 (t0) cc_final: 0.7585 (p0) REVERT: D 71 GLN cc_start: 0.9290 (tt0) cc_final: 0.9074 (tp40) REVERT: D 72 PHE cc_start: 0.9612 (t80) cc_final: 0.9010 (t80) REVERT: D 86 THR cc_start: 0.9399 (m) cc_final: 0.9185 (t) REVERT: D 89 ASN cc_start: 0.9423 (m-40) cc_final: 0.8997 (p0) REVERT: D 105 MET cc_start: 0.9169 (mtt) cc_final: 0.8788 (mmm) REVERT: E 31 PHE cc_start: 0.9381 (m-80) cc_final: 0.8782 (m-10) REVERT: E 41 ASP cc_start: 0.7730 (m-30) cc_final: 0.7523 (m-30) REVERT: E 62 LYS cc_start: 0.9535 (mtmt) cc_final: 0.9125 (tptt) REVERT: E 65 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8815 (tm-30) REVERT: E 69 ARG cc_start: 0.9065 (ptp90) cc_final: 0.8828 (ptt180) REVERT: E 71 MET cc_start: 0.8582 (mtp) cc_final: 0.6821 (mtp) REVERT: E 86 LYS cc_start: 0.9226 (mmtm) cc_final: 0.8825 (tptt) REVERT: E 116 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8880 (tm-30) REVERT: F 21 MET cc_start: 0.9159 (ptp) cc_final: 0.8724 (ptm) REVERT: F 62 MET cc_start: 0.8990 (mtm) cc_final: 0.8693 (mpp) REVERT: F 88 MET cc_start: 0.8647 (tmm) cc_final: 0.7044 (tmm) REVERT: F 100 SER cc_start: 0.9089 (m) cc_final: 0.8848 (p) REVERT: H 45 PHE cc_start: 0.8366 (m-80) cc_final: 0.6443 (m-80) REVERT: H 121 LEU cc_start: 0.8904 (mt) cc_final: 0.8641 (tt) REVERT: I 111 VAL cc_start: 0.8826 (p) cc_final: 0.8364 (t) REVERT: I 112 GLU cc_start: 0.6842 (tt0) cc_final: 0.5582 (mp0) REVERT: I 116 VAL cc_start: 0.8568 (t) cc_final: 0.8127 (t) REVERT: J 52 LEU cc_start: 0.8528 (mt) cc_final: 0.8203 (mt) REVERT: K 85 MET cc_start: 0.8577 (mtp) cc_final: 0.8161 (mpp) REVERT: L 112 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8599 (mp10) REVERT: L 117 TYR cc_start: 0.8747 (m-80) cc_final: 0.8510 (m-80) REVERT: M 23 TYR cc_start: 0.6910 (t80) cc_final: 0.6325 (t80) REVERT: N 14 VAL cc_start: 0.9108 (t) cc_final: 0.8832 (t) REVERT: N 39 GLU cc_start: 0.8841 (tp30) cc_final: 0.8639 (tm-30) REVERT: P 12 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8419 (tmmt) REVERT: Q 8 LEU cc_start: 0.9549 (tp) cc_final: 0.9193 (tp) REVERT: Q 15 ASP cc_start: 0.8917 (p0) cc_final: 0.8630 (p0) REVERT: Q 69 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8484 (ttpt) REVERT: R 22 ASP cc_start: 0.7633 (t0) cc_final: 0.7318 (t0) REVERT: R 25 ASP cc_start: 0.8156 (t0) cc_final: 0.7803 (t0) REVERT: R 60 LYS cc_start: 0.9396 (mttt) cc_final: 0.9072 (mtpp) REVERT: R 61 ARG cc_start: 0.8974 (mtt180) cc_final: 0.8320 (mmt90) REVERT: R 67 LEU cc_start: 0.9432 (mp) cc_final: 0.9176 (mt) REVERT: R 68 LEU cc_start: 0.8806 (mm) cc_final: 0.8500 (mt) REVERT: V 49 TYR cc_start: 0.8117 (m-80) cc_final: 0.7875 (m-10) REVERT: V 51 LYS cc_start: 0.9183 (mtpt) cc_final: 0.8861 (mmtm) REVERT: V 62 GLU cc_start: 0.8748 (tp30) cc_final: 0.8447 (tp30) REVERT: X 124 MET cc_start: 0.8894 (mmm) cc_final: 0.8300 (mmm) outliers start: 0 outliers final: 0 residues processed: 618 average time/residue: 0.7599 time to fit residues: 729.7868 Evaluate side-chains 359 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 338 optimal weight: 0.5980 chunk 303 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 205 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 314 optimal weight: 6.9990 chunk 121 optimal weight: 30.0000 chunk 191 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 364 optimal weight: 8.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 122 GLN B 227 GLN ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 40 GLN D 126 ASN G 68 ASN G 122 ASN ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN L 72 HIS N 4 GLN O 37 ASN O 38 HIS O 42 HIS P 29 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN R 52 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 56978 Z= 0.242 Angle : 0.719 13.491 84400 Z= 0.377 Chirality : 0.038 0.271 10651 Planarity : 0.006 0.118 5111 Dihedral : 25.091 179.492 26451 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 33.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.47 % Allowed : 5.81 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.16), residues: 2550 helix: -0.59 (0.15), residues: 1006 sheet: -1.17 (0.23), residues: 442 loop : -1.37 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP X 113 HIS 0.006 0.001 HIS X 56 PHE 0.037 0.002 PHE N 21 TYR 0.032 0.002 TYR D 76 ARG 0.015 0.001 ARG H 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 482 time to evaluate : 3.284 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: 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: symmetry clash REVERT: B 62 SER cc_start: 0.7360 (p) cc_final: 0.7159 (p) REVERT: B 64 LYS cc_start: 0.7394 (mttp) cc_final: 0.7101 (tppt) REVERT: B 109 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: B 140 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 142 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8802 (tm-30) REVERT: B 144 LEU cc_start: 0.9027 (mt) cc_final: 0.8534 (mt) REVERT: B 189 THR cc_start: 0.4010 (p) cc_final: 0.3386 (p) REVERT: B 222 ARG cc_start: 0.6591 (ptp-170) cc_final: 0.5887 (ptp-170) REVERT: C 25 ASN cc_start: 0.9495 (t0) cc_final: 0.9276 (t0) REVERT: C 29 PHE cc_start: 0.9089 (t80) cc_final: 0.8708 (t80) REVERT: C 181 ASP cc_start: 0.8785 (t0) cc_final: 0.7642 (p0) REVERT: C 211 MET cc_start: 0.4383 (mmt) cc_final: 0.4087 (mmt) REVERT: D 72 PHE cc_start: 0.9616 (t80) cc_final: 0.9068 (t80) REVERT: D 86 THR cc_start: 0.9372 (m) cc_final: 0.8910 (t) REVERT: D 89 ASN cc_start: 0.9381 (m-40) cc_final: 0.8943 (p0) REVERT: D 124 MET cc_start: 0.8439 (mmp) cc_final: 0.7311 (mtt) REVERT: D 204 TYR cc_start: 0.8448 (m-80) cc_final: 0.7768 (m-10) REVERT: E 29 ARG cc_start: 0.7547 (mtt-85) cc_final: 0.7264 (mtt-85) REVERT: E 31 PHE cc_start: 0.9254 (m-80) cc_final: 0.9045 (m-10) REVERT: E 61 GLN cc_start: 0.9741 (tp-100) cc_final: 0.9440 (tm-30) REVERT: E 86 LYS cc_start: 0.9156 (mmtm) cc_final: 0.8828 (tptt) REVERT: E 96 MET cc_start: 0.9375 (mmp) cc_final: 0.9149 (mmp) REVERT: F 21 MET cc_start: 0.9143 (ptp) cc_final: 0.8054 (ptm) REVERT: F 88 MET cc_start: 0.8567 (tmm) cc_final: 0.8239 (tmm) REVERT: F 98 GLU cc_start: 0.7847 (pp20) cc_final: 0.7386 (pp20) REVERT: F 104 LYS cc_start: 0.9371 (ptpp) cc_final: 0.9025 (pttt) REVERT: G 31 MET cc_start: 0.4117 (ttp) cc_final: 0.3484 (ptm) REVERT: H 27 MET cc_start: 0.9480 (pmm) cc_final: 0.9119 (pmm) REVERT: H 59 LEU cc_start: 0.9533 (tp) cc_final: 0.9282 (tp) REVERT: H 105 SER cc_start: 0.9424 (t) cc_final: 0.9157 (p) REVERT: H 121 LEU cc_start: 0.8639 (mt) cc_final: 0.8167 (tt) REVERT: I 42 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8454 (tp30) REVERT: I 111 VAL cc_start: 0.8929 (p) cc_final: 0.8515 (t) REVERT: I 112 GLU cc_start: 0.6635 (tt0) cc_final: 0.5505 (mp0) REVERT: J 49 PHE cc_start: 0.8709 (m-10) cc_final: 0.8493 (m-10) REVERT: J 63 ASP cc_start: 0.8099 (t70) cc_final: 0.7822 (t0) REVERT: J 65 TYR cc_start: 0.8755 (m-10) cc_final: 0.8131 (m-10) REVERT: L 38 TYR cc_start: 0.9227 (p90) cc_final: 0.8568 (p90) REVERT: L 70 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8365 (mp0) REVERT: L 81 LEU cc_start: 0.9161 (mm) cc_final: 0.8780 (mm) REVERT: L 104 CYS cc_start: 0.8563 (m) cc_final: 0.8278 (m) REVERT: L 112 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8737 (mp10) REVERT: L 117 TYR cc_start: 0.8633 (m-80) cc_final: 0.8324 (m-80) REVERT: M 23 TYR cc_start: 0.7358 (t80) cc_final: 0.6628 (t80) REVERT: P 1 MET cc_start: 0.7854 (ttp) cc_final: 0.7211 (tmm) REVERT: P 12 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8411 (tmmt) REVERT: P 26 ASN cc_start: 0.9044 (m110) cc_final: 0.8674 (m110) REVERT: P 48 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8478 (tp30) REVERT: Q 17 MET cc_start: 0.8228 (mpp) cc_final: 0.7677 (mpp) REVERT: Q 69 LYS cc_start: 0.8780 (tptt) cc_final: 0.8570 (tmmt) REVERT: R 50 LYS cc_start: 0.9424 (ptmt) cc_final: 0.9185 (ptmm) REVERT: R 54 GLN cc_start: 0.8934 (mt0) cc_final: 0.8661 (mt0) REVERT: R 60 LYS cc_start: 0.9440 (mttt) cc_final: 0.9230 (mtpp) REVERT: R 61 ARG cc_start: 0.8909 (mtt180) cc_final: 0.8690 (ttm110) REVERT: R 67 LEU cc_start: 0.9487 (mp) cc_final: 0.9262 (mt) REVERT: R 68 LEU cc_start: 0.8999 (mm) cc_final: 0.8666 (mt) REVERT: T 86 LEU cc_start: 0.8170 (mm) cc_final: 0.7813 (mm) REVERT: V 43 MET cc_start: 0.7520 (pmm) cc_final: 0.6982 (pmm) REVERT: V 49 TYR cc_start: 0.8341 (m-80) cc_final: 0.7746 (m-10) REVERT: V 62 GLU cc_start: 0.8732 (tp30) cc_final: 0.8388 (tp30) REVERT: X 44 ASP cc_start: 0.8250 (t0) cc_final: 0.8050 (t0) REVERT: X 150 PHE cc_start: 0.7853 (t80) cc_final: 0.7329 (t80) outliers start: 10 outliers final: 5 residues processed: 490 average time/residue: 0.7246 time to fit residues: 563.7677 Evaluate side-chains 332 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 326 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 202 optimal weight: 10.0000 chunk 113 optimal weight: 30.0000 chunk 303 optimal weight: 20.0000 chunk 247 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 364 optimal weight: 40.0000 chunk 394 optimal weight: 20.0000 chunk 324 optimal weight: 5.9990 chunk 361 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 292 optimal weight: 9.9990 overall best weight: 13.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN D 40 GLN E 83 HIS H 18 GLN ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN K 81 ASN ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN O 80 GLN ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 ASN ** V 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 56978 Z= 0.480 Angle : 0.914 12.926 84400 Z= 0.465 Chirality : 0.045 0.266 10651 Planarity : 0.008 0.124 5111 Dihedral : 25.325 179.731 26451 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 57.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.14 % Allowed : 8.65 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.98 (0.15), residues: 2550 helix: -0.94 (0.15), residues: 1008 sheet: -1.51 (0.23), residues: 449 loop : -1.42 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP P 60 HIS 0.013 0.003 HIS Q 47 PHE 0.025 0.003 PHE B 90 TYR 0.027 0.003 TYR D 75 ARG 0.021 0.001 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 371 time to evaluate : 3.359 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: 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 64 LYS cc_start: 0.7631 (mttp) cc_final: 0.7427 (tppt) REVERT: B 118 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7641 (pp20) REVERT: B 140 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 144 LEU cc_start: 0.8717 (mt) cc_final: 0.8350 (mt) REVERT: C 130 PHE cc_start: 0.9180 (p90) cc_final: 0.8875 (p90) REVERT: C 181 ASP cc_start: 0.8950 (t0) cc_final: 0.7712 (p0) REVERT: D 72 PHE cc_start: 0.9674 (t80) cc_final: 0.9033 (t80) REVERT: D 124 MET cc_start: 0.8512 (mmp) cc_final: 0.7779 (mmt) REVERT: E 31 PHE cc_start: 0.9087 (m-80) cc_final: 0.8778 (m-10) REVERT: E 71 MET cc_start: 0.8136 (ttt) cc_final: 0.7233 (ttt) REVERT: E 93 ARG cc_start: 0.8994 (mpt180) cc_final: 0.8679 (mpt180) REVERT: F 21 MET cc_start: 0.8992 (ptp) cc_final: 0.7994 (ptm) REVERT: F 88 MET cc_start: 0.8898 (tmm) cc_final: 0.7359 (tmm) REVERT: F 104 LYS cc_start: 0.9395 (ptpp) cc_final: 0.9181 (ptpt) REVERT: G 136 LYS cc_start: 0.8007 (tptp) cc_final: 0.7446 (mmtp) REVERT: H 59 LEU cc_start: 0.9426 (tp) cc_final: 0.9211 (tp) REVERT: I 112 GLU cc_start: 0.6556 (tt0) cc_final: 0.5262 (mp0) REVERT: J 8 ILE cc_start: 0.8172 (tp) cc_final: 0.7882 (mp) REVERT: J 49 PHE cc_start: 0.8909 (m-10) cc_final: 0.8617 (m-10) REVERT: J 52 LEU cc_start: 0.8773 (mm) cc_final: 0.8358 (tp) REVERT: J 97 ASP cc_start: 0.8052 (t0) cc_final: 0.6559 (t0) REVERT: L 38 TYR cc_start: 0.9237 (p90) cc_final: 0.8664 (p90) REVERT: L 112 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8715 (mp10) REVERT: M 3 ARG cc_start: 0.8117 (mmp-170) cc_final: 0.7613 (pmt170) REVERT: N 101 TRP cc_start: 0.7470 (p90) cc_final: 0.6528 (p90) REVERT: P 1 MET cc_start: 0.8037 (ttp) cc_final: 0.7214 (tmm) REVERT: P 12 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8763 (ttpt) REVERT: P 26 ASN cc_start: 0.9213 (m110) cc_final: 0.8915 (m110) REVERT: P 48 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8696 (tm-30) REVERT: Q 17 MET cc_start: 0.8463 (mpp) cc_final: 0.7934 (mpp) REVERT: Q 27 ARG cc_start: 0.9096 (ptt-90) cc_final: 0.8559 (ptt-90) REVERT: Q 69 LYS cc_start: 0.8996 (tptt) cc_final: 0.8785 (tmmt) REVERT: R 22 ASP cc_start: 0.8139 (t70) cc_final: 0.7915 (t0) REVERT: R 50 LYS cc_start: 0.9442 (ptmt) cc_final: 0.8953 (ptmm) REVERT: S 81 ARG cc_start: 0.8181 (mpp-170) cc_final: 0.7824 (mtt90) REVERT: T 27 MET cc_start: 0.9335 (tmm) cc_final: 0.9052 (ttm) REVERT: V 43 MET cc_start: 0.8514 (pmm) cc_final: 0.7664 (pmm) REVERT: X 124 MET cc_start: 0.8950 (mmm) cc_final: 0.8551 (mmm) outliers start: 3 outliers final: 1 residues processed: 374 average time/residue: 0.7568 time to fit residues: 451.1570 Evaluate side-chains 262 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 260 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 360 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 366 optimal weight: 5.9990 chunk 387 optimal weight: 5.9990 chunk 191 optimal weight: 30.0000 chunk 346 optimal weight: 7.9990 chunk 104 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN D 40 GLN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN H 18 GLN ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN ** V 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 56978 Z= 0.249 Angle : 0.688 12.589 84400 Z= 0.363 Chirality : 0.037 0.251 10651 Planarity : 0.006 0.120 5111 Dihedral : 25.117 179.934 26451 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 38.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.16), residues: 2550 helix: -0.51 (0.15), residues: 1010 sheet: -1.34 (0.23), residues: 458 loop : -1.17 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 96 HIS 0.013 0.002 HIS F 58 PHE 0.031 0.002 PHE C 37 TYR 0.038 0.002 TYR R 23 ARG 0.020 0.001 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 388 time to evaluate : 3.369 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: 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 64 LYS cc_start: 0.7778 (mttp) cc_final: 0.7502 (tppt) REVERT: B 140 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8389 (tm-30) REVERT: B 144 LEU cc_start: 0.8840 (mt) cc_final: 0.8355 (mt) REVERT: C 29 PHE cc_start: 0.9072 (t80) cc_final: 0.8811 (t80) REVERT: C 130 PHE cc_start: 0.9116 (p90) cc_final: 0.8810 (p90) REVERT: C 134 MET cc_start: 0.8782 (ptp) cc_final: 0.8313 (ptm) REVERT: C 181 ASP cc_start: 0.8668 (t0) cc_final: 0.7374 (p0) REVERT: D 72 PHE cc_start: 0.9620 (t80) cc_final: 0.8983 (t80) REVERT: D 75 TYR cc_start: 0.8922 (m-80) cc_final: 0.8465 (m-80) REVERT: D 124 MET cc_start: 0.8280 (mmp) cc_final: 0.7701 (mmt) REVERT: D 204 TYR cc_start: 0.8417 (m-10) cc_final: 0.8011 (m-10) REVERT: E 14 LYS cc_start: 0.9167 (mptt) cc_final: 0.8912 (mmtp) REVERT: E 29 ARG cc_start: 0.7691 (mtt-85) cc_final: 0.7388 (mtt-85) REVERT: E 31 PHE cc_start: 0.9227 (m-80) cc_final: 0.8978 (m-10) REVERT: E 45 ARG cc_start: 0.8422 (ttt-90) cc_final: 0.7720 (ttt-90) REVERT: E 71 MET cc_start: 0.8127 (ttt) cc_final: 0.7097 (ttt) REVERT: E 86 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8793 (tptp) REVERT: E 96 MET cc_start: 0.9541 (mmp) cc_final: 0.9314 (mmp) REVERT: F 21 MET cc_start: 0.9046 (ptp) cc_final: 0.8102 (ptm) REVERT: F 68 GLN cc_start: 0.9148 (pm20) cc_final: 0.8380 (tt0) REVERT: F 88 MET cc_start: 0.8767 (tmm) cc_final: 0.7196 (tmm) REVERT: F 90 MET cc_start: 0.8988 (tpp) cc_final: 0.8728 (tpp) REVERT: G 136 LYS cc_start: 0.7991 (tptp) cc_final: 0.7439 (mmtp) REVERT: H 59 LEU cc_start: 0.9544 (tp) cc_final: 0.9308 (tp) REVERT: H 101 ILE cc_start: 0.8815 (mm) cc_final: 0.8517 (mm) REVERT: I 111 VAL cc_start: 0.9091 (p) cc_final: 0.8633 (t) REVERT: I 112 GLU cc_start: 0.6422 (tt0) cc_final: 0.5269 (mp0) REVERT: J 49 PHE cc_start: 0.8836 (m-10) cc_final: 0.8540 (m-10) REVERT: J 52 LEU cc_start: 0.8550 (mm) cc_final: 0.8223 (tp) REVERT: K 85 MET cc_start: 0.8211 (mmp) cc_final: 0.7903 (mmp) REVERT: L 38 TYR cc_start: 0.9144 (p90) cc_final: 0.8591 (p90) REVERT: L 112 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8715 (mp10) REVERT: M 65 VAL cc_start: 0.8395 (p) cc_final: 0.8136 (t) REVERT: N 79 LEU cc_start: 0.9070 (tp) cc_final: 0.8739 (mt) REVERT: N 89 MET cc_start: 0.9063 (tpp) cc_final: 0.8857 (tpp) REVERT: P 1 MET cc_start: 0.8000 (ttp) cc_final: 0.7259 (tmm) REVERT: P 12 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8488 (ttpp) REVERT: P 26 ASN cc_start: 0.9176 (m110) cc_final: 0.8893 (m110) REVERT: P 48 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8770 (tp30) REVERT: Q 15 ASP cc_start: 0.8828 (p0) cc_final: 0.8621 (p0) REVERT: Q 17 MET cc_start: 0.8321 (mpp) cc_final: 0.7345 (mpp) REVERT: Q 69 LYS cc_start: 0.8983 (tptt) cc_final: 0.8733 (tmmt) REVERT: R 50 LYS cc_start: 0.9436 (ptmt) cc_final: 0.9094 (ptmm) REVERT: R 61 ARG cc_start: 0.8997 (mtt180) cc_final: 0.8567 (mmt90) REVERT: R 64 TYR cc_start: 0.9153 (t80) cc_final: 0.8789 (t80) REVERT: R 68 LEU cc_start: 0.9095 (tp) cc_final: 0.8820 (tp) REVERT: S 81 ARG cc_start: 0.8105 (mpp-170) cc_final: 0.7726 (mtt90) REVERT: T 27 MET cc_start: 0.9190 (tmm) cc_final: 0.8865 (tmm) REVERT: V 42 GLU cc_start: 0.9296 (pp20) cc_final: 0.8907 (pm20) REVERT: V 49 TYR cc_start: 0.8767 (m-80) cc_final: 0.8470 (m-80) REVERT: X 149 HIS cc_start: 0.6975 (t-90) cc_final: 0.6769 (t-90) outliers start: 1 outliers final: 1 residues processed: 389 average time/residue: 0.7107 time to fit residues: 444.3885 Evaluate side-chains 295 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 322 optimal weight: 0.0270 chunk 220 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 288 optimal weight: 20.0000 chunk 159 optimal weight: 7.9990 chunk 330 optimal weight: 30.0000 chunk 267 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 347 optimal weight: 20.0000 chunk 97 optimal weight: 50.0000 overall best weight: 8.0048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 56978 Z= 0.315 Angle : 0.731 12.467 84400 Z= 0.382 Chirality : 0.038 0.250 10651 Planarity : 0.007 0.122 5111 Dihedral : 25.063 179.998 26451 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 45.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.57 (0.16), residues: 2550 helix: -0.60 (0.15), residues: 1008 sheet: -1.30 (0.23), residues: 445 loop : -1.18 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 96 HIS 0.013 0.002 HIS P 59 PHE 0.067 0.003 PHE G 26 TYR 0.024 0.002 TYR H 128 ARG 0.015 0.001 ARG P 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 369 time to evaluate : 3.245 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 SER cc_start: 0.7172 (p) cc_final: 0.6872 (p) REVERT: C 29 PHE cc_start: 0.9126 (t80) cc_final: 0.8918 (t80) REVERT: C 130 PHE cc_start: 0.9175 (p90) cc_final: 0.8869 (p90) REVERT: C 134 MET cc_start: 0.8876 (ptp) cc_final: 0.8121 (ptp) REVERT: C 181 ASP cc_start: 0.8463 (t0) cc_final: 0.7363 (p0) REVERT: D 72 PHE cc_start: 0.9653 (t80) cc_final: 0.9012 (t80) REVERT: D 75 TYR cc_start: 0.9041 (m-80) cc_final: 0.8507 (m-80) REVERT: D 105 MET cc_start: 0.9290 (mtp) cc_final: 0.8665 (mmm) REVERT: E 71 MET cc_start: 0.8195 (ttt) cc_final: 0.7803 (ttt) REVERT: E 86 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8807 (tptp) REVERT: E 88 VAL cc_start: 0.8935 (t) cc_final: 0.8098 (t) REVERT: E 96 MET cc_start: 0.9545 (mmp) cc_final: 0.9310 (mmp) REVERT: E 115 LEU cc_start: 0.9497 (mp) cc_final: 0.9272 (mp) REVERT: F 21 MET cc_start: 0.9071 (ptp) cc_final: 0.8656 (ptm) REVERT: F 62 MET cc_start: 0.8405 (mpp) cc_final: 0.8203 (mpp) REVERT: F 73 GLU cc_start: 0.9558 (OUTLIER) cc_final: 0.9287 (pm20) REVERT: G 136 LYS cc_start: 0.8044 (tptp) cc_final: 0.7480 (mmtp) REVERT: H 5 ASP cc_start: 0.8374 (t70) cc_final: 0.8018 (t0) REVERT: H 59 LEU cc_start: 0.9556 (tp) cc_final: 0.9333 (tp) REVERT: H 86 TYR cc_start: 0.8381 (m-80) cc_final: 0.8180 (m-80) REVERT: H 101 ILE cc_start: 0.8968 (mm) cc_final: 0.8730 (mm) REVERT: I 111 VAL cc_start: 0.9103 (p) cc_final: 0.8713 (t) REVERT: I 112 GLU cc_start: 0.6530 (tt0) cc_final: 0.5323 (mp0) REVERT: I 118 LEU cc_start: 0.9433 (mt) cc_final: 0.9224 (mt) REVERT: I 129 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8378 (mmmt) REVERT: J 49 PHE cc_start: 0.8836 (m-10) cc_final: 0.8554 (m-10) REVERT: J 52 LEU cc_start: 0.8553 (mm) cc_final: 0.8228 (tp) REVERT: J 63 ASP cc_start: 0.8102 (t70) cc_final: 0.7741 (t70) REVERT: J 65 TYR cc_start: 0.9079 (m-80) cc_final: 0.8337 (m-10) REVERT: K 85 MET cc_start: 0.8137 (mmp) cc_final: 0.7868 (mmm) REVERT: L 38 TYR cc_start: 0.9157 (p90) cc_final: 0.8604 (p90) REVERT: L 112 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8781 (mp10) REVERT: M 65 VAL cc_start: 0.8462 (p) cc_final: 0.8189 (t) REVERT: N 77 PHE cc_start: 0.8867 (m-80) cc_final: 0.8589 (m-80) REVERT: N 89 MET cc_start: 0.9113 (tpp) cc_final: 0.8837 (tpp) REVERT: P 1 MET cc_start: 0.8111 (ttp) cc_final: 0.7218 (tmm) REVERT: P 12 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8591 (ttpp) REVERT: P 26 ASN cc_start: 0.9105 (m110) cc_final: 0.8879 (m110) REVERT: P 48 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8682 (tm-30) REVERT: Q 17 MET cc_start: 0.8273 (mpp) cc_final: 0.7879 (mpp) REVERT: R 50 LYS cc_start: 0.9411 (ptmt) cc_final: 0.8955 (ptmm) REVERT: R 61 ARG cc_start: 0.8929 (mtt180) cc_final: 0.8529 (mmt90) REVERT: R 64 TYR cc_start: 0.9191 (t80) cc_final: 0.8628 (t80) REVERT: R 68 LEU cc_start: 0.9274 (tp) cc_final: 0.9035 (tp) REVERT: S 81 ARG cc_start: 0.8224 (mpp-170) cc_final: 0.7725 (mtt90) REVERT: T 27 MET cc_start: 0.9227 (tmm) cc_final: 0.8916 (tmm) REVERT: X 12 ILE cc_start: 0.9414 (mm) cc_final: 0.9213 (mm) outliers start: 2 outliers final: 1 residues processed: 371 average time/residue: 0.7133 time to fit residues: 424.3020 Evaluate side-chains 265 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 130 optimal weight: 30.0000 chunk 349 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 387 optimal weight: 0.9990 chunk 322 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 128 optimal weight: 30.0000 chunk 203 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 HIS ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 71 HIS ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 56978 Z= 0.223 Angle : 0.654 12.521 84400 Z= 0.346 Chirality : 0.035 0.251 10651 Planarity : 0.006 0.120 5111 Dihedral : 24.933 179.516 26451 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 36.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.32 (0.16), residues: 2550 helix: -0.40 (0.15), residues: 1006 sheet: -1.15 (0.23), residues: 442 loop : -1.05 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 113 HIS 0.007 0.001 HIS C 6 PHE 0.036 0.002 PHE G 26 TYR 0.025 0.002 TYR X 39 ARG 0.010 0.001 ARG H 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 3.019 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.6458 (tp) cc_final: 0.6030 (tt) REVERT: C 29 PHE cc_start: 0.9106 (t80) cc_final: 0.8896 (t80) REVERT: C 130 PHE cc_start: 0.9154 (p90) cc_final: 0.8846 (p90) REVERT: C 134 MET cc_start: 0.8801 (ptp) cc_final: 0.7964 (ptp) REVERT: C 142 MET cc_start: 0.8478 (mmt) cc_final: 0.7286 (mmm) REVERT: C 181 ASP cc_start: 0.8442 (t0) cc_final: 0.7374 (p0) REVERT: D 72 PHE cc_start: 0.9628 (t80) cc_final: 0.8898 (t80) REVERT: D 75 TYR cc_start: 0.9011 (m-80) cc_final: 0.8475 (m-80) REVERT: D 105 MET cc_start: 0.9274 (mtp) cc_final: 0.8635 (mmm) REVERT: D 124 MET cc_start: 0.8019 (mpp) cc_final: 0.7759 (mpp) REVERT: E 96 MET cc_start: 0.9495 (mmp) cc_final: 0.9286 (mmm) REVERT: F 21 MET cc_start: 0.9095 (ptp) cc_final: 0.8319 (ptm) REVERT: H 59 LEU cc_start: 0.9562 (tp) cc_final: 0.9357 (tp) REVERT: H 101 ILE cc_start: 0.8941 (mm) cc_final: 0.8693 (mm) REVERT: I 46 MET cc_start: 0.7541 (mmm) cc_final: 0.6840 (tmm) REVERT: I 111 VAL cc_start: 0.9080 (p) cc_final: 0.8442 (t) REVERT: I 112 GLU cc_start: 0.6464 (tt0) cc_final: 0.5123 (mp0) REVERT: I 118 LEU cc_start: 0.9463 (mt) cc_final: 0.9262 (mt) REVERT: I 129 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8319 (mmmt) REVERT: J 49 PHE cc_start: 0.8856 (m-10) cc_final: 0.8592 (m-10) REVERT: J 52 LEU cc_start: 0.8568 (mm) cc_final: 0.8228 (tp) REVERT: K 85 MET cc_start: 0.8114 (mmp) cc_final: 0.7795 (mmp) REVERT: L 38 TYR cc_start: 0.9143 (p90) cc_final: 0.8489 (p90) REVERT: L 112 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8733 (mp10) REVERT: M 65 VAL cc_start: 0.8414 (p) cc_final: 0.8143 (t) REVERT: N 14 VAL cc_start: 0.8769 (t) cc_final: 0.8555 (t) REVERT: N 89 MET cc_start: 0.9206 (tpp) cc_final: 0.8974 (tpp) REVERT: P 1 MET cc_start: 0.7992 (ttp) cc_final: 0.7116 (tmm) REVERT: P 12 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8500 (ttpp) REVERT: P 26 ASN cc_start: 0.9064 (m110) cc_final: 0.8862 (m110) REVERT: P 48 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8675 (tm-30) REVERT: P 80 LYS cc_start: 0.9581 (tttt) cc_final: 0.9338 (mmtm) REVERT: Q 17 MET cc_start: 0.8243 (mpp) cc_final: 0.7978 (mpp) REVERT: Q 25 ILE cc_start: 0.8889 (mp) cc_final: 0.8647 (mp) REVERT: R 50 LYS cc_start: 0.9367 (ptmt) cc_final: 0.9047 (ptmm) REVERT: R 61 ARG cc_start: 0.8971 (mtt180) cc_final: 0.8478 (mmt90) REVERT: R 64 TYR cc_start: 0.9169 (t80) cc_final: 0.8634 (t80) REVERT: R 68 LEU cc_start: 0.9264 (tp) cc_final: 0.9034 (tp) REVERT: S 81 ARG cc_start: 0.8141 (mpp-170) cc_final: 0.7664 (mtt90) REVERT: T 27 MET cc_start: 0.9263 (tmm) cc_final: 0.9014 (tmm) REVERT: V 43 MET cc_start: 0.8770 (pmm) cc_final: 0.7762 (ppp) REVERT: V 47 LEU cc_start: 0.9406 (tp) cc_final: 0.9168 (tp) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.6773 time to fit residues: 399.0576 Evaluate side-chains 283 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 374 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 219 optimal weight: 2.9990 chunk 326 optimal weight: 0.0570 chunk 216 optimal weight: 10.0000 chunk 386 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 56978 Z= 0.207 Angle : 0.632 12.425 84400 Z= 0.336 Chirality : 0.034 0.310 10651 Planarity : 0.006 0.120 5111 Dihedral : 24.775 179.625 26451 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 34.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.16), residues: 2550 helix: -0.25 (0.16), residues: 1005 sheet: -0.93 (0.24), residues: 438 loop : -0.97 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP G 103 HIS 0.007 0.001 HIS C 6 PHE 0.038 0.002 PHE G 26 TYR 0.038 0.002 TYR D 76 ARG 0.013 0.001 ARG J 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 2.713 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.6696 (tp) cc_final: 0.6344 (tt) REVERT: B 21 ARG cc_start: 0.4052 (tpm170) cc_final: 0.3744 (tpm170) REVERT: C 130 PHE cc_start: 0.9178 (p90) cc_final: 0.8843 (p90) REVERT: C 134 MET cc_start: 0.8819 (ptp) cc_final: 0.8010 (ptp) REVERT: C 142 MET cc_start: 0.8393 (mmt) cc_final: 0.7242 (mmm) REVERT: C 181 ASP cc_start: 0.8425 (t0) cc_final: 0.7493 (p0) REVERT: D 72 PHE cc_start: 0.9645 (t80) cc_final: 0.8976 (t80) REVERT: D 75 TYR cc_start: 0.9073 (m-80) cc_final: 0.8466 (m-80) REVERT: D 124 MET cc_start: 0.8077 (mpp) cc_final: 0.7651 (mpp) REVERT: E 36 LEU cc_start: 0.9380 (mm) cc_final: 0.9132 (mm) REVERT: E 65 GLU cc_start: 0.9687 (tt0) cc_final: 0.9443 (tt0) REVERT: E 66 LYS cc_start: 0.9441 (mmtm) cc_final: 0.8868 (mmmt) REVERT: E 115 LEU cc_start: 0.9531 (mt) cc_final: 0.9214 (mt) REVERT: F 21 MET cc_start: 0.9057 (ptp) cc_final: 0.8214 (ptm) REVERT: F 90 MET cc_start: 0.8994 (tpp) cc_final: 0.8740 (tpp) REVERT: H 59 LEU cc_start: 0.9573 (tp) cc_final: 0.9365 (tp) REVERT: H 101 ILE cc_start: 0.8943 (mm) cc_final: 0.8729 (mt) REVERT: I 46 MET cc_start: 0.7193 (mmm) cc_final: 0.6557 (tmm) REVERT: I 111 VAL cc_start: 0.8976 (p) cc_final: 0.8673 (t) REVERT: I 112 GLU cc_start: 0.6328 (tt0) cc_final: 0.5012 (mp0) REVERT: J 49 PHE cc_start: 0.8835 (m-10) cc_final: 0.8634 (m-10) REVERT: J 52 LEU cc_start: 0.8512 (mm) cc_final: 0.8106 (tp) REVERT: K 85 MET cc_start: 0.8068 (mmp) cc_final: 0.7767 (mmp) REVERT: L 38 TYR cc_start: 0.9217 (p90) cc_final: 0.8552 (p90) REVERT: L 112 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8755 (mp10) REVERT: M 65 VAL cc_start: 0.8377 (p) cc_final: 0.8093 (t) REVERT: N 14 VAL cc_start: 0.8761 (t) cc_final: 0.8547 (t) REVERT: P 1 MET cc_start: 0.7941 (ttp) cc_final: 0.7107 (tmm) REVERT: P 48 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8709 (tp30) REVERT: P 80 LYS cc_start: 0.9579 (tttt) cc_final: 0.9367 (mmtm) REVERT: Q 17 MET cc_start: 0.8238 (mpp) cc_final: 0.7959 (mpp) REVERT: R 50 LYS cc_start: 0.9323 (ptmt) cc_final: 0.8768 (ptmm) REVERT: R 61 ARG cc_start: 0.8953 (mtt180) cc_final: 0.8454 (mmt90) REVERT: R 64 TYR cc_start: 0.9165 (t80) cc_final: 0.8574 (t80) REVERT: R 68 LEU cc_start: 0.9289 (tp) cc_final: 0.9081 (tp) REVERT: T 27 MET cc_start: 0.9280 (tmm) cc_final: 0.8991 (tmm) REVERT: V 47 LEU cc_start: 0.9464 (tp) cc_final: 0.9201 (tt) REVERT: V 66 LYS cc_start: 0.9825 (tppt) cc_final: 0.9463 (pttt) REVERT: V 91 ILE cc_start: 0.8348 (mp) cc_final: 0.8088 (mp) REVERT: X 37 ARG cc_start: 0.8733 (mtp-110) cc_final: 0.8510 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.7393 time to fit residues: 447.9816 Evaluate side-chains 285 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 239 optimal weight: 20.0000 chunk 154 optimal weight: 0.0070 chunk 230 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 245 optimal weight: 20.0000 chunk 263 optimal weight: 0.0030 chunk 191 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 303 optimal weight: 9.9990 overall best weight: 5.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS N 66 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 56978 Z= 0.230 Angle : 0.649 15.852 84400 Z= 0.344 Chirality : 0.035 0.241 10651 Planarity : 0.006 0.121 5111 Dihedral : 24.748 179.815 26451 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 35.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.07 (0.16), residues: 2550 helix: -0.26 (0.16), residues: 1009 sheet: -0.90 (0.25), residues: 423 loop : -0.89 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.135 0.004 TRP G 103 HIS 0.008 0.002 HIS E 89 PHE 0.023 0.002 PHE D 107 TYR 0.030 0.002 TYR H 86 ARG 0.017 0.001 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.657 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.7519 (ppt170) cc_final: 0.6987 (tmm160) REVERT: B 10 LEU cc_start: 0.6882 (tp) cc_final: 0.6492 (tt) REVERT: C 130 PHE cc_start: 0.9191 (p90) cc_final: 0.8849 (p90) REVERT: C 134 MET cc_start: 0.8813 (ptp) cc_final: 0.7975 (ptp) REVERT: C 142 MET cc_start: 0.8472 (mmt) cc_final: 0.7334 (mmm) REVERT: C 168 TYR cc_start: 0.8224 (t80) cc_final: 0.8014 (t80) REVERT: D 72 PHE cc_start: 0.9656 (t80) cc_final: 0.8831 (t80) REVERT: D 105 MET cc_start: 0.9368 (mmp) cc_final: 0.8925 (mmm) REVERT: D 124 MET cc_start: 0.8081 (mpp) cc_final: 0.7723 (mpp) REVERT: E 36 LEU cc_start: 0.9364 (mm) cc_final: 0.9145 (mm) REVERT: E 65 GLU cc_start: 0.9681 (tt0) cc_final: 0.9424 (tt0) REVERT: E 66 LYS cc_start: 0.9462 (mmtm) cc_final: 0.8949 (mmmt) REVERT: E 86 LYS cc_start: 0.9155 (tptp) cc_final: 0.8820 (tptp) REVERT: F 21 MET cc_start: 0.9044 (ptp) cc_final: 0.8162 (ptm) REVERT: F 90 MET cc_start: 0.8958 (tpp) cc_final: 0.8739 (mmm) REVERT: G 103 TRP cc_start: 0.3431 (m-90) cc_final: 0.3103 (m-90) REVERT: G 136 LYS cc_start: 0.8083 (tptp) cc_final: 0.7806 (mmtp) REVERT: H 59 LEU cc_start: 0.9555 (tp) cc_final: 0.9350 (tp) REVERT: H 101 ILE cc_start: 0.8972 (mm) cc_final: 0.8725 (mt) REVERT: I 31 ASN cc_start: 0.7306 (m110) cc_final: 0.7100 (m-40) REVERT: I 46 MET cc_start: 0.7543 (mmm) cc_final: 0.6897 (tmm) REVERT: I 57 MET cc_start: 0.1906 (mtp) cc_final: 0.1582 (mtm) REVERT: I 111 VAL cc_start: 0.8968 (p) cc_final: 0.8600 (t) REVERT: I 112 GLU cc_start: 0.6279 (tt0) cc_final: 0.5013 (mp0) REVERT: J 42 LEU cc_start: 0.9053 (mp) cc_final: 0.8632 (mt) REVERT: J 49 PHE cc_start: 0.8878 (m-10) cc_final: 0.8614 (m-10) REVERT: J 52 LEU cc_start: 0.8525 (mm) cc_final: 0.8101 (tp) REVERT: K 75 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8927 (mmmt) REVERT: K 85 MET cc_start: 0.8080 (mmp) cc_final: 0.7783 (mmp) REVERT: L 38 TYR cc_start: 0.9252 (p90) cc_final: 0.8569 (p90) REVERT: L 112 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8748 (mp10) REVERT: M 65 VAL cc_start: 0.8447 (p) cc_final: 0.8179 (t) REVERT: P 48 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8730 (tp30) REVERT: Q 15 ASP cc_start: 0.8810 (p0) cc_final: 0.8593 (p0) REVERT: Q 17 MET cc_start: 0.8084 (mpp) cc_final: 0.7867 (mpp) REVERT: Q 25 ILE cc_start: 0.8892 (mp) cc_final: 0.8680 (mp) REVERT: R 50 LYS cc_start: 0.9331 (ptmt) cc_final: 0.8777 (ptmm) REVERT: R 61 ARG cc_start: 0.8948 (mtt180) cc_final: 0.8492 (mmt90) REVERT: R 64 TYR cc_start: 0.9149 (t80) cc_final: 0.8573 (t80) REVERT: R 65 LEU cc_start: 0.9806 (mt) cc_final: 0.9569 (mt) REVERT: T 27 MET cc_start: 0.9217 (tmm) cc_final: 0.8959 (tmm) REVERT: V 47 LEU cc_start: 0.9451 (tp) cc_final: 0.9208 (tt) REVERT: V 91 ILE cc_start: 0.8395 (mp) cc_final: 0.8097 (mp) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.6708 time to fit residues: 395.9865 Evaluate side-chains 282 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 351 optimal weight: 6.9990 chunk 370 optimal weight: 8.9990 chunk 337 optimal weight: 10.0000 chunk 360 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 340 optimal weight: 10.0000 chunk 358 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 110 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 56978 Z= 0.212 Angle : 0.642 20.837 84400 Z= 0.340 Chirality : 0.034 0.239 10651 Planarity : 0.006 0.121 5111 Dihedral : 24.694 179.570 26451 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 34.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.94 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.16), residues: 2550 helix: -0.22 (0.16), residues: 1007 sheet: -0.91 (0.24), residues: 428 loop : -0.84 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP G 103 HIS 0.017 0.002 HIS M 14 PHE 0.023 0.002 PHE C 37 TYR 0.024 0.002 TYR D 76 ARG 0.012 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 3.085 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.7010 (tp) cc_final: 0.6717 (tt) REVERT: C 130 PHE cc_start: 0.9161 (p90) cc_final: 0.8782 (p90) REVERT: C 134 MET cc_start: 0.8748 (ptp) cc_final: 0.7931 (ptp) REVERT: C 168 TYR cc_start: 0.8212 (t80) cc_final: 0.8001 (t80) REVERT: C 181 ASP cc_start: 0.8441 (t70) cc_final: 0.7694 (p0) REVERT: D 72 PHE cc_start: 0.9612 (t80) cc_final: 0.9062 (t80) REVERT: D 75 TYR cc_start: 0.8973 (m-80) cc_final: 0.8613 (m-80) REVERT: D 105 MET cc_start: 0.9325 (mmp) cc_final: 0.8865 (mmm) REVERT: D 124 MET cc_start: 0.8065 (mpp) cc_final: 0.7733 (mpp) REVERT: E 36 LEU cc_start: 0.9361 (mm) cc_final: 0.9144 (mm) REVERT: E 65 GLU cc_start: 0.9680 (tt0) cc_final: 0.9310 (tt0) REVERT: E 66 LYS cc_start: 0.9507 (mmtm) cc_final: 0.8908 (mmmt) REVERT: E 86 LYS cc_start: 0.9109 (tptp) cc_final: 0.8741 (tptp) REVERT: E 97 GLN cc_start: 0.9439 (tp40) cc_final: 0.9153 (tp40) REVERT: E 115 LEU cc_start: 0.9512 (mt) cc_final: 0.9231 (mt) REVERT: F 21 MET cc_start: 0.8953 (ptp) cc_final: 0.8065 (ptm) REVERT: F 90 MET cc_start: 0.9021 (tpp) cc_final: 0.8804 (mmm) REVERT: G 136 LYS cc_start: 0.8159 (tptp) cc_final: 0.7487 (mmtp) REVERT: G 137 LYS cc_start: 0.7056 (tppt) cc_final: 0.6676 (tttt) REVERT: H 59 LEU cc_start: 0.9575 (tp) cc_final: 0.9370 (tp) REVERT: H 96 MET cc_start: 0.9299 (mpp) cc_final: 0.9058 (mpp) REVERT: H 101 ILE cc_start: 0.8949 (mm) cc_final: 0.8626 (mt) REVERT: I 31 ASN cc_start: 0.7361 (m110) cc_final: 0.7139 (m-40) REVERT: I 46 MET cc_start: 0.7264 (mmm) cc_final: 0.6713 (tmm) REVERT: I 57 MET cc_start: 0.1696 (mtp) cc_final: 0.1377 (mtm) REVERT: I 111 VAL cc_start: 0.8993 (p) cc_final: 0.8629 (t) REVERT: I 112 GLU cc_start: 0.6230 (tt0) cc_final: 0.4966 (mp0) REVERT: I 118 LEU cc_start: 0.9628 (mm) cc_final: 0.9356 (mt) REVERT: J 42 LEU cc_start: 0.9048 (mp) cc_final: 0.8639 (mt) REVERT: J 49 PHE cc_start: 0.8891 (m-10) cc_final: 0.8596 (m-10) REVERT: J 52 LEU cc_start: 0.8556 (mm) cc_final: 0.8099 (tp) REVERT: J 88 MET cc_start: 0.8692 (mpp) cc_final: 0.8415 (mpp) REVERT: K 75 LYS cc_start: 0.9132 (mmpt) cc_final: 0.8901 (mmmt) REVERT: K 85 MET cc_start: 0.8078 (mmp) cc_final: 0.7757 (mmp) REVERT: L 38 TYR cc_start: 0.9252 (p90) cc_final: 0.8552 (p90) REVERT: L 112 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8774 (mp10) REVERT: M 65 VAL cc_start: 0.8551 (p) cc_final: 0.8285 (t) REVERT: P 12 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8502 (ttpp) REVERT: P 48 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8706 (tp30) REVERT: Q 15 ASP cc_start: 0.8807 (p0) cc_final: 0.8583 (p0) REVERT: Q 17 MET cc_start: 0.8021 (mpp) cc_final: 0.7784 (mpp) REVERT: R 50 LYS cc_start: 0.9357 (ptmt) cc_final: 0.9007 (pttp) REVERT: R 61 ARG cc_start: 0.8922 (mtt180) cc_final: 0.8478 (mmt90) REVERT: R 64 TYR cc_start: 0.9158 (t80) cc_final: 0.8575 (t80) REVERT: R 65 LEU cc_start: 0.9791 (mt) cc_final: 0.9530 (mt) REVERT: T 27 MET cc_start: 0.9233 (tmm) cc_final: 0.8986 (tmm) REVERT: T 86 LEU cc_start: 0.8355 (mm) cc_final: 0.7859 (mt) REVERT: V 35 MET cc_start: 0.8169 (ppp) cc_final: 0.7706 (ppp) REVERT: V 47 LEU cc_start: 0.9428 (tp) cc_final: 0.9176 (tt) REVERT: V 91 ILE cc_start: 0.8324 (mp) cc_final: 0.8039 (mp) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.5957 time to fit residues: 345.6045 Evaluate side-chains 290 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 236 optimal weight: 3.9990 chunk 380 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 399 optimal weight: 9.9990 chunk 367 optimal weight: 2.9990 chunk 318 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 245 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 56978 Z= 0.212 Angle : 0.641 17.914 84400 Z= 0.339 Chirality : 0.034 0.272 10651 Planarity : 0.006 0.121 5111 Dihedral : 24.645 179.574 26451 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 34.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.16), residues: 2550 helix: -0.23 (0.16), residues: 1013 sheet: -0.91 (0.24), residues: 428 loop : -0.78 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.003 TRP G 103 HIS 0.008 0.001 HIS C 6 PHE 0.023 0.002 PHE V 97 TYR 0.034 0.002 TYR D 76 ARG 0.012 0.001 ARG P 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 2.554 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: 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: B 10 LEU cc_start: 0.7079 (tp) cc_final: 0.6765 (tt) REVERT: C 130 PHE cc_start: 0.9172 (p90) cc_final: 0.8785 (p90) REVERT: C 134 MET cc_start: 0.8787 (ptp) cc_final: 0.7954 (ptp) REVERT: C 142 MET cc_start: 0.8453 (mmt) cc_final: 0.7657 (mmm) REVERT: C 168 TYR cc_start: 0.8202 (t80) cc_final: 0.7986 (t80) REVERT: C 181 ASP cc_start: 0.8509 (t70) cc_final: 0.7701 (p0) REVERT: D 72 PHE cc_start: 0.9660 (t80) cc_final: 0.9082 (t80) REVERT: D 75 TYR cc_start: 0.9079 (m-80) cc_final: 0.8707 (m-80) REVERT: D 105 MET cc_start: 0.9324 (mmp) cc_final: 0.8894 (mmm) REVERT: D 124 MET cc_start: 0.8018 (mpp) cc_final: 0.7705 (mpp) REVERT: E 65 GLU cc_start: 0.9652 (tt0) cc_final: 0.9382 (tt0) REVERT: E 66 LYS cc_start: 0.9534 (mmtm) cc_final: 0.9092 (mmmt) REVERT: E 72 ILE cc_start: 0.9318 (pt) cc_final: 0.9065 (pt) REVERT: E 86 LYS cc_start: 0.9105 (tptp) cc_final: 0.8856 (tptt) REVERT: F 21 MET cc_start: 0.8975 (ptp) cc_final: 0.8016 (ptm) REVERT: F 90 MET cc_start: 0.9019 (tpp) cc_final: 0.8806 (mmm) REVERT: G 136 LYS cc_start: 0.8033 (tptp) cc_final: 0.7489 (mmtp) REVERT: H 96 MET cc_start: 0.9323 (mpp) cc_final: 0.9010 (mpp) REVERT: H 99 LEU cc_start: 0.9607 (mt) cc_final: 0.9365 (mt) REVERT: H 101 ILE cc_start: 0.8954 (mm) cc_final: 0.8651 (mt) REVERT: I 31 ASN cc_start: 0.7365 (m110) cc_final: 0.7135 (m-40) REVERT: I 46 MET cc_start: 0.7500 (mmm) cc_final: 0.6899 (tmm) REVERT: I 118 LEU cc_start: 0.9649 (mm) cc_final: 0.9369 (mt) REVERT: J 42 LEU cc_start: 0.9004 (mp) cc_final: 0.8636 (mt) REVERT: J 49 PHE cc_start: 0.8901 (m-10) cc_final: 0.8592 (m-10) REVERT: J 52 LEU cc_start: 0.8592 (mm) cc_final: 0.8150 (tp) REVERT: J 88 MET cc_start: 0.8662 (mpp) cc_final: 0.8362 (mpp) REVERT: K 75 LYS cc_start: 0.9111 (mmpt) cc_final: 0.8820 (mmmt) REVERT: L 38 TYR cc_start: 0.9230 (p90) cc_final: 0.8524 (p90) REVERT: L 112 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8773 (mp10) REVERT: M 65 VAL cc_start: 0.8541 (p) cc_final: 0.8265 (t) REVERT: P 12 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8759 (ttmt) REVERT: P 48 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8684 (tp30) REVERT: P 56 ARG cc_start: 0.9152 (tpm170) cc_final: 0.8786 (mmm160) REVERT: Q 15 ASP cc_start: 0.8816 (p0) cc_final: 0.8606 (p0) REVERT: Q 17 MET cc_start: 0.8002 (mpp) cc_final: 0.7774 (mpp) REVERT: Q 27 ARG cc_start: 0.9048 (ptt-90) cc_final: 0.8659 (ptt-90) REVERT: R 50 LYS cc_start: 0.9340 (ptmt) cc_final: 0.9002 (pttp) REVERT: R 61 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8497 (mmt90) REVERT: R 64 TYR cc_start: 0.9156 (t80) cc_final: 0.8646 (t80) REVERT: R 65 LEU cc_start: 0.9791 (mt) cc_final: 0.9576 (mt) REVERT: T 27 MET cc_start: 0.9207 (tmm) cc_final: 0.8974 (tmm) REVERT: V 34 MET cc_start: 0.7858 (ptm) cc_final: 0.7598 (ppp) REVERT: V 47 LEU cc_start: 0.9418 (tp) cc_final: 0.9153 (tt) REVERT: V 91 ILE cc_start: 0.8257 (mp) cc_final: 0.7980 (mp) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.6011 time to fit residues: 353.4665 Evaluate side-chains 282 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 252 optimal weight: 20.0000 chunk 338 optimal weight: 10.0000 chunk 97 optimal weight: 50.0000 chunk 293 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 318 optimal weight: 0.0050 chunk 133 optimal weight: 30.0000 chunk 327 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 overall best weight: 9.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS N 71 HIS ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.028386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.019742 restraints weight = 847043.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.020335 restraints weight = 438238.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.020761 restraints weight = 298164.240| |-----------------------------------------------------------------------------| r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 56978 Z= 0.362 Angle : 0.784 16.398 84400 Z= 0.405 Chirality : 0.040 0.240 10651 Planarity : 0.007 0.123 5111 Dihedral : 24.907 179.593 26451 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 48.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.47 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.16), residues: 2550 helix: -0.58 (0.15), residues: 1033 sheet: -1.21 (0.24), residues: 444 loop : -1.08 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.004 TRP G 103 HIS 0.011 0.002 HIS K 118 PHE 0.036 0.003 PHE B 90 TYR 0.040 0.003 TYR H 86 ARG 0.010 0.001 ARG B 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9004.89 seconds wall clock time: 166 minutes 25.01 seconds (9985.01 seconds total)