Starting phenix.real_space_refine on Mon Feb 19 13:28:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/02_2024/6ddg_7870_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/02_2024/6ddg_7870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/02_2024/6ddg_7870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/02_2024/6ddg_7870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/02_2024/6ddg_7870_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/02_2024/6ddg_7870_trim_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.008 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 P 2747 5.49 5 S 55 5.16 5 Cl 1 4.86 5 C 39210 2.51 5 N 14779 2.21 5 O 22791 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "I ARG 79": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "L ARG 86": "NH1" <-> "NH2" Residue "L ARG 92": "NH1" <-> "NH2" Residue "L ARG 138": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "N ARG 6": "NH1" <-> "NH2" Residue "N ARG 7": "NH1" <-> "NH2" Residue "O ARG 15": "NH1" <-> "NH2" Residue "P ARG 4": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 22": "NH1" <-> "NH2" Residue "P ARG 34": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 57": "NH1" <-> "NH2" Residue "S ARG 54": "NH1" <-> "NH2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S ARG 106": "NH1" <-> "NH2" Residue "S ARG 107": "NH1" <-> "NH2" Residue "S ARG 168": "NH1" <-> "NH2" Residue "V ARG 2": "NH1" <-> "NH2" Residue "V ARG 14": "NH1" <-> "NH2" Residue "V ARG 38": "NH1" <-> "NH2" Residue "V ARG 144": "NH1" <-> "NH2" Residue "Y ARG 10": "NH1" <-> "NH2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ARG 56": "NH1" <-> "NH2" Residue "Y ARG 60": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" 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: 79584 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 915 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "B" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2063 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 17, 'TRANS': 252} Chain breaks: 1 Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "F" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 684 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "G" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 697 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 597 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "J" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 449 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "K" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 463 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 397 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "P" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Q" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "R" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "S" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1441 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain: "V" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1138 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "W" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "X" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1082 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "Y" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "Z" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 955 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain: "a" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 787 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain breaks: 2 Chain: "1" Number of atoms: 56747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2646, 56747 Inner-chain residues flagged as termini: ['pdbres=" A 11459 "', 'pdbres=" G 11556 "'] Classifications: {'RNA': 2646} Modifications used: {'5*END': 3, 'rna2p_pur': 266, 'rna2p_pyr': 132, 'rna3p_pur': 1258, 'rna3p_pyr': 990} Link IDs: {'rna2p': 398, 'rna3p': 2247} Chain breaks: 9 Chain: "2" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2214 Classifications: {'RNA': 104} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 45} Link IDs: {'rna2p': 13, 'rna3p': 90} Chain: "1" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'G6M': 1} Classifications: {'undetermined': 1} Time building chain proxies: 34.60, per 1000 atoms: 0.43 Number of scatterers: 79584 At special positions: 0 Unit cell: (201.4, 221.54, 182.32, 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) Cl 1 17.00 S 55 16.00 P 2747 15.00 F 1 9.00 O 22791 8.00 N 14779 7.00 C 39210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 43 " distance=2.04 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 27 " distance=2.04 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=0, symmetry=0 Time building additional restraints: 34.08 Conformation dependent library (CDL) restraints added in 3.9 seconds 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4782 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 36 sheets defined 21.6% alpha, 15.3% beta 817 base pairs and 1454 stacking pairs defined. Time for finding SS restraints: 38.14 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 198 through 202 removed outlier: 4.112A pdb=" N GLU B 201 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'C' and resid 8 through 18 removed outlier: 3.522A pdb=" N ALA C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 29 Processing helix chain 'C' and resid 32 through 69 removed outlier: 3.911A pdb=" N GLN C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG C 55 " --> pdb=" O ARG C 51 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'E' and resid 14 through 24 removed outlier: 4.396A pdb=" N LEU E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 38 removed outlier: 3.732A pdb=" N ILE E 33 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 59 removed outlier: 4.102A pdb=" N VAL E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 22 removed outlier: 3.623A pdb=" N ALA F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 46 Processing helix chain 'H' and resid 15 through 22 Processing helix chain 'H' and resid 47 through 55 removed outlier: 4.272A pdb=" N GLU H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'J' and resid 51 through 54 removed outlier: 3.787A pdb=" N LEU J 54 " --> pdb=" O ALA J 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 51 through 54' Processing helix chain 'K' and resid 11 through 21 Processing helix chain 'K' and resid 23 through 33 Processing helix chain 'K' and resid 40 through 59 removed outlier: 4.498A pdb=" N ARG K 47 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU K 53 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL K 56 " --> pdb=" O LEU K 53 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU K 59 " --> pdb=" O VAL K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 79 Processing helix chain 'L' and resid 107 through 109 No H-bonds generated for 'chain 'L' and resid 107 through 109' Processing helix chain 'L' and resid 130 through 134 Processing helix chain 'M' and resid 17 through 26 Processing helix chain 'M' and resid 46 through 49 No H-bonds generated for 'chain 'M' and resid 46 through 49' Processing helix chain 'N' and resid 10 through 18 removed outlier: 3.742A pdb=" N ASN N 14 " --> pdb=" O LYS N 10 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR N 18 " --> pdb=" O ASN N 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 17 Processing helix chain 'P' and resid 19 through 22 No H-bonds generated for 'chain 'P' and resid 19 through 22' Processing helix chain 'P' and resid 26 through 38 removed outlier: 3.618A pdb=" N LYS P 38 " --> pdb=" O ARG P 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 13 removed outlier: 3.999A pdb=" N LYS Q 12 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG Q 13 " --> pdb=" O GLY Q 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 8 through 13' Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 38 through 41 No H-bonds generated for 'chain 'Q' and resid 38 through 41' Processing helix chain 'Q' and resid 52 through 57 Processing helix chain 'R' and resid 30 through 32 No H-bonds generated for 'chain 'R' and resid 30 through 32' Processing helix chain 'S' and resid 30 through 44 removed outlier: 3.779A pdb=" N GLU S 35 " --> pdb=" O SER S 31 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU S 44 " --> pdb=" O GLN S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 119 removed outlier: 3.902A pdb=" N LEU S 114 " --> pdb=" O LEU S 110 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 146 Processing helix chain 'S' and resid 161 through 167 removed outlier: 3.518A pdb=" N LEU S 165 " --> pdb=" O VAL S 161 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER S 166 " --> pdb=" O ASN S 162 " (cutoff:3.500A) Processing helix chain 'S' and resid 178 through 180 No H-bonds generated for 'chain 'S' and resid 178 through 180' Processing helix chain 'S' and resid 183 through 188 removed outlier: 3.676A pdb=" N THR S 187 " --> pdb=" O VAL S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 198 through 205 Processing helix chain 'V' and resid 26 through 38 removed outlier: 4.116A pdb=" N GLU V 32 " --> pdb=" O ARG V 28 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE V 36 " --> pdb=" O GLU V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 62 No H-bonds generated for 'chain 'V' and resid 60 through 62' Processing helix chain 'V' and resid 91 through 94 No H-bonds generated for 'chain 'V' and resid 91 through 94' Processing helix chain 'V' and resid 98 through 109 removed outlier: 4.125A pdb=" N GLU V 103 " --> pdb=" O GLU V 99 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET V 109 " --> pdb=" O SER V 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 122 removed outlier: 3.786A pdb=" N LYS V 121 " --> pdb=" O GLU V 117 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS V 122 " --> pdb=" O LYS V 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 106 No H-bonds generated for 'chain 'W' and resid 104 through 106' Processing helix chain 'W' and resid 112 through 117 Processing helix chain 'X' and resid 131 through 139 removed outlier: 4.076A pdb=" N LYS X 139 " --> pdb=" O ALA X 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 57 removed outlier: 3.615A pdb=" N SER Y 49 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 122 Processing helix chain 'Z' and resid 10 through 27 Processing helix chain 'Z' and resid 34 through 53 removed outlier: 4.392A pdb=" N SER Z 42 " --> pdb=" O LYS Z 38 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS Z 46 " --> pdb=" O SER Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 64 removed outlier: 3.729A pdb=" N LYS Z 64 " --> pdb=" O ARG Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 81 through 92 removed outlier: 4.145A pdb=" N ILE Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA Z 90 " --> pdb=" O PHE Z 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 20 removed outlier: 4.078A pdb=" N LYS a 13 " --> pdb=" O LYS a 9 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR a 20 " --> pdb=" O ALA a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 87 Processing helix chain 'a' and resid 104 through 112 removed outlier: 3.914A pdb=" N ALA a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 86 through 90 removed outlier: 6.797A pdb=" N THR A 27 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N GLU A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 66 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR A 62 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR A 60 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 3 through 5 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 105 removed outlier: 3.638A pdb=" N ILE B 91 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 95 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL B 78 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'B' and resid 171 through 175 Processing sheet with id= F, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.469A pdb=" N GLU D 6 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL D 38 " --> pdb=" O GLU D 6 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 19 through 23 Processing sheet with id= H, first strand: chain 'D' and resid 71 through 77 removed outlier: 4.341A pdb=" N SER D 82 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 59 through 62 removed outlier: 6.235A pdb=" N THR D 61 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE D 97 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 2 through 7 removed outlier: 6.670A pdb=" N SER E 108 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL E 71 " --> pdb=" O SER E 108 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 82 through 86 Processing sheet with id= L, first strand: chain 'F' and resid 7 through 10 removed outlier: 6.481A pdb=" N ASP F 28 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N THR F 26 " --> pdb=" O PRO F 10 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 40 through 43 Processing sheet with id= N, first strand: chain 'G' and resid 81 through 85 Processing sheet with id= O, first strand: chain 'H' and resid 41 through 44 removed outlier: 9.978A pdb=" N GLN H 85 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR H 87 " --> pdb=" O PRO H 28 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N VAL H 30 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE H 89 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N TYR H 32 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE H 91 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLN H 78 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 59 through 61 Processing sheet with id= Q, first strand: chain 'I' and resid 74 through 79 Processing sheet with id= R, first strand: chain 'J' and resid 13 through 18 Processing sheet with id= S, first strand: chain 'J' and resid 33 through 38 Processing sheet with id= T, first strand: chain 'L' and resid 177 through 180 removed outlier: 4.673A pdb=" N VAL L 121 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU L 208 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL L 27 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET L 12 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL L 25 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN L 14 " --> pdb=" O ILE L 23 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE L 23 " --> pdb=" O GLN L 14 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN L 187 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS L 198 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL L 185 " --> pdb=" O LYS L 198 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 88 through 91 removed outlier: 3.848A pdb=" N ALA L 48 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN L 37 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY L 52 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL L 35 " --> pdb=" O GLY L 52 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 34 through 36 Processing sheet with id= W, first strand: chain 'N' and resid 27 through 29 Processing sheet with id= X, first strand: chain 'O' and resid 32 through 36 Processing sheet with id= Y, first strand: chain 'Q' and resid 14 through 16 removed outlier: 3.694A pdb=" N LYS Q 15 " --> pdb=" O LYS Q 23 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'R' and resid 15 through 19 Processing sheet with id= AA, first strand: chain 'S' and resid 173 through 177 removed outlier: 6.484A pdb=" N VAL S 152 " --> pdb=" O GLN S 174 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR S 176 " --> pdb=" O VAL S 152 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL S 154 " --> pdb=" O THR S 176 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'V' and resid 16 through 20 removed outlier: 6.577A pdb=" N TYR V 54 " --> pdb=" O TYR V 17 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ILE V 19 " --> pdb=" O TYR V 54 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE V 56 " --> pdb=" O ILE V 19 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'V' and resid 74 through 78 Processing sheet with id= AD, first strand: chain 'W' and resid 7 through 9 removed outlier: 6.867A pdb=" N VAL W 40 " --> pdb=" O ILE W 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL W 24 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL W 38 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS W 59 " --> pdb=" O ILE W 87 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA W 83 " --> pdb=" O VAL W 63 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'X' and resid 75 through 77 Processing sheet with id= AF, first strand: chain 'X' and resid 88 through 91 removed outlier: 3.654A pdb=" N THR X 122 " --> pdb=" O GLY X 88 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU X 90 " --> pdb=" O THR X 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'Y' and resid 129 through 133 removed outlier: 3.952A pdb=" N PHE Y 104 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA Y 36 " --> pdb=" O ILE Y 102 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE Y 102 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Y' and resid 40 through 43 removed outlier: 7.001A pdb=" N TYR Y 74 " --> pdb=" O GLU Y 91 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TRP Y 93 " --> pdb=" O THR Y 72 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR Y 72 " --> pdb=" O TRP Y 93 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'Z' and resid 29 through 33 removed outlier: 3.716A pdb=" N GLY Z 107 " --> pdb=" O SER Z 116 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE Z 118 " --> pdb=" O LYS Z 105 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS Z 105 " --> pdb=" O ILE Z 118 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'a' and resid 30 through 32 491 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2056 hydrogen bonds 3320 hydrogen bond angles 0 basepair planarities 817 basepair parallelities 1454 stacking parallelities Total time for adding SS restraints: 110.18 Time building geometry restraints manager: 36.77 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: 12563 1.33 - 1.46: 38494 1.46 - 1.58: 30326 1.58 - 1.71: 5429 1.71 - 1.83: 97 Bond restraints: 86909 Sorted by residual: bond pdb=" C12 G6M 13001 " pdb=" O11 G6M 13001 " ideal model delta sigma weight residual 1.339 1.447 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C1' U 2 68 " pdb=" N1 U 2 68 " ideal model delta sigma weight residual 1.480 1.561 -0.081 1.50e-02 4.44e+03 2.91e+01 bond pdb=" C12 G6M 13001 " pdb=" N8 G6M 13001 " ideal model delta sigma weight residual 1.364 1.311 0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" C ARG M 20 " pdb=" O ARG M 20 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.22e+00 bond pdb=" O5' A 11926 " pdb=" C5' A 11926 " ideal model delta sigma weight residual 1.420 1.451 -0.031 1.50e-02 4.44e+03 4.18e+00 ... (remaining 86904 not shown) Histogram of bond angle deviations from ideal: 92.09 - 100.49: 116 100.49 - 108.90: 33664 108.90 - 117.30: 47570 117.30 - 125.71: 39783 125.71 - 134.11: 9741 Bond angle restraints: 130874 Sorted by residual: angle pdb=" O2' C 2 91 " pdb=" C2' C 2 91 " pdb=" C1' C 2 91 " ideal model delta sigma weight residual 108.40 92.09 16.31 1.50e+00 4.44e-01 1.18e+02 angle pdb=" O2' G 11924 " pdb=" C2' G 11924 " pdb=" C1' G 11924 " ideal model delta sigma weight residual 108.40 92.42 15.98 1.50e+00 4.44e-01 1.13e+02 angle pdb=" O2' A 11954 " pdb=" C2' A 11954 " pdb=" C1' A 11954 " ideal model delta sigma weight residual 108.40 92.54 15.86 1.50e+00 4.44e-01 1.12e+02 angle pdb=" O2' U 2 90 " pdb=" C2' U 2 90 " pdb=" C1' U 2 90 " ideal model delta sigma weight residual 108.40 94.60 13.80 1.50e+00 4.44e-01 8.46e+01 angle pdb=" C4' G 11867 " pdb=" C3' G 11867 " pdb=" O3' G 11867 " ideal model delta sigma weight residual 113.00 125.16 -12.16 1.50e+00 4.44e-01 6.58e+01 ... (remaining 130869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 48663 35.95 - 71.89: 6160 71.89 - 107.84: 668 107.84 - 143.78: 20 143.78 - 179.73: 37 Dihedral angle restraints: 55548 sinusoidal: 48104 harmonic: 7444 Sorted by residual: dihedral pdb=" O4' U 1 403 " pdb=" C1' U 1 403 " pdb=" N1 U 1 403 " pdb=" C2 U 1 403 " ideal model delta sinusoidal sigma weight residual 200.00 20.27 179.73 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 12607 " pdb=" C1' U 12607 " pdb=" N1 U 12607 " pdb=" C2 U 12607 " ideal model delta sinusoidal sigma weight residual -160.00 18.46 -178.46 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 12639 " pdb=" C1' C 12639 " pdb=" N1 C 12639 " pdb=" C2 C 12639 " ideal model delta sinusoidal sigma weight residual 200.00 23.60 176.40 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 55545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 15374 0.075 - 0.150: 1353 0.150 - 0.226: 114 0.226 - 0.301: 18 0.301 - 0.376: 4 Chirality restraints: 16863 Sorted by residual: chirality pdb=" C1' A 1 125 " pdb=" O4' A 1 125 " pdb=" C2' A 1 125 " pdb=" N9 A 1 125 " both_signs ideal model delta sigma weight residual False 2.46 2.08 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C3' G 11930 " pdb=" C4' G 11930 " pdb=" O3' G 11930 " pdb=" C2' G 11930 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C3' G 11866 " pdb=" C4' G 11866 " pdb=" O3' G 11866 " pdb=" C2' G 11866 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 16860 not shown) Planarity restraints: 6328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 11867 " -0.040 2.00e-02 2.50e+03 2.33e-02 1.63e+01 pdb=" N9 G 11867 " 0.068 2.00e-02 2.50e+03 pdb=" C8 G 11867 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G 11867 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G 11867 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G 11867 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G 11867 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G 11867 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G 11867 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 11867 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G 11867 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G 11867 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 557 " 0.048 2.00e-02 2.50e+03 2.08e-02 1.30e+01 pdb=" N9 G 1 557 " -0.050 2.00e-02 2.50e+03 pdb=" C8 G 1 557 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G 1 557 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 1 557 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G 1 557 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G 1 557 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G 1 557 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G 1 557 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G 1 557 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 1 557 " -0.011 2.00e-02 2.50e+03 pdb=" C4 G 1 557 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 2 91 " 0.035 2.00e-02 2.50e+03 2.20e-02 1.08e+01 pdb=" N1 C 2 91 " -0.055 2.00e-02 2.50e+03 pdb=" C2 C 2 91 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C 2 91 " -0.000 2.00e-02 2.50e+03 pdb=" N3 C 2 91 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C 2 91 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C 2 91 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C 2 91 " 0.005 2.00e-02 2.50e+03 pdb=" C6 C 2 91 " -0.000 2.00e-02 2.50e+03 ... (remaining 6325 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1822 2.61 - 3.18: 63194 3.18 - 3.76: 154035 3.76 - 4.33: 223947 4.33 - 4.90: 294905 Nonbonded interactions: 737903 Sorted by model distance: nonbonded pdb=" OH TYR Y 57 " pdb=" OE1 GLU Y 116 " model vdw 2.040 2.440 nonbonded pdb=" O2' U 11510 " pdb=" O4' C 11511 " model vdw 2.040 2.440 nonbonded pdb=" OP1 U 11063 " pdb=" O2' U 11079 " model vdw 2.044 2.440 nonbonded pdb=" O2' A 1 645 " pdb=" O2' G 1 647 " model vdw 2.044 2.440 nonbonded pdb=" O2' A 12740 " pdb=" OP2 C 12742 " model vdw 2.049 2.440 ... (remaining 737898 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 12.850 Check model and map are aligned: 0.940 Set scattering table: 0.560 Process input model: 272.100 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 294.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.007 0.108 86909 Z= 0.419 Angle : 0.779 16.314 130874 Z= 0.414 Chirality : 0.044 0.376 16863 Planarity : 0.005 0.059 6328 Dihedral : 23.682 179.725 50760 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.05 % Allowed : 3.14 % Favored : 96.82 % 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: -4.42 (0.13), residues: 2575 helix: -2.72 (0.16), residues: 625 sheet: -2.67 (0.20), residues: 480 loop : -3.22 (0.13), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.005 TRP B 213 HIS 0.013 0.002 HIS B 53 PHE 0.042 0.003 PHE K 30 TYR 0.040 0.003 TYR F 58 ARG 0.023 0.002 ARG X 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 739 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7141 (mtm180) cc_final: 0.6711 (mtt180) REVERT: B 77 LYS cc_start: 0.7533 (tppt) cc_final: 0.7303 (tptt) REVERT: B 171 TYR cc_start: 0.8141 (m-80) cc_final: 0.7642 (m-80) REVERT: D 81 ASN cc_start: 0.7442 (m-40) cc_final: 0.7241 (m-40) REVERT: E 27 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8403 (mmtm) REVERT: F 49 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7602 (mmmm) REVERT: F 65 MET cc_start: 0.4649 (ptm) cc_final: 0.4297 (mmm) REVERT: H 18 LEU cc_start: 0.8369 (mt) cc_final: 0.8096 (mt) REVERT: H 23 LYS cc_start: 0.7528 (mptp) cc_final: 0.7162 (tptt) REVERT: I 84 LYS cc_start: 0.7915 (mttp) cc_final: 0.7602 (mtmm) REVERT: K 14 ILE cc_start: 0.7447 (mm) cc_final: 0.7106 (tt) REVERT: K 20 SER cc_start: 0.8587 (m) cc_final: 0.8365 (m) REVERT: M 44 ARG cc_start: 0.7720 (tpp80) cc_final: 0.7519 (mmm-85) REVERT: O 1 MET cc_start: 0.4680 (ptp) cc_final: 0.4337 (mtp) REVERT: O 40 ASN cc_start: 0.8435 (t0) cc_final: 0.8137 (t0) REVERT: W 5 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7723 (mm-30) REVERT: W 31 LYS cc_start: 0.8234 (pmmt) cc_final: 0.8034 (ptpp) REVERT: X 15 GLU cc_start: 0.6374 (pt0) cc_final: 0.5869 (mt-10) REVERT: Z 89 ILE cc_start: 0.8710 (mm) cc_final: 0.8318 (mt) REVERT: a 38 LYS cc_start: 0.6578 (pttt) cc_final: 0.6296 (mptt) REVERT: a 99 TYR cc_start: 0.7084 (m-80) cc_final: 0.6805 (m-80) outliers start: 1 outliers final: 1 residues processed: 740 average time/residue: 0.8793 time to fit residues: 1052.2087 Evaluate side-chains 554 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 553 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 6.9990 chunk 400 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 213 optimal weight: 0.0170 chunk 413 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 251 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 chunk 479 optimal weight: 5.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 4 HIS ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 70 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS C 37 GLN C 38 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN E 57 ASN E 65 ASN F 54 ASN G 44 HIS H 38 ASN H 85 GLN H 88 HIS J 16 ASN K 17 GLN K 27 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 HIS L 146 HIS M 52 HIS ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 GLN P 9 ASN P 17 HIS Q 7 HIS Q 31 HIS Q 35 ASN S 29 ASN S 46 GLN S 75 GLN S 141 ASN S 148 GLN S 169 ASN S 188 ASN V 8 ASN V 24 GLN V 48 HIS X 4 HIS X 17 ASN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 71 HIS Z 83 GLN ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 86909 Z= 0.428 Angle : 0.790 11.811 130874 Z= 0.395 Chirality : 0.046 0.369 16863 Planarity : 0.007 0.072 6328 Dihedral : 24.215 179.925 45447 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.41 % Allowed : 11.46 % Favored : 85.13 % 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: -3.61 (0.14), residues: 2575 helix: -1.89 (0.18), residues: 624 sheet: -2.23 (0.21), residues: 504 loop : -2.76 (0.13), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 213 HIS 0.011 0.002 HIS A 4 PHE 0.040 0.003 PHE Z 86 TYR 0.032 0.003 TYR F 58 ARG 0.009 0.001 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 539 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7020 (mtm180) cc_final: 0.6676 (mtt180) REVERT: B 77 LYS cc_start: 0.7778 (tppt) cc_final: 0.7488 (tptp) REVERT: D 18 GLN cc_start: 0.7793 (tt0) cc_final: 0.7387 (tt0) REVERT: E 90 GLN cc_start: 0.8313 (mt0) cc_final: 0.8025 (mt0) REVERT: F 65 MET cc_start: 0.4404 (ptm) cc_final: 0.4078 (mmm) REVERT: H 37 LYS cc_start: 0.5964 (ttpt) cc_final: 0.5695 (tttm) REVERT: I 84 LYS cc_start: 0.7936 (mttp) cc_final: 0.7652 (mtmm) REVERT: K 14 ILE cc_start: 0.7522 (mm) cc_final: 0.6966 (tt) REVERT: L 116 ILE cc_start: 0.8781 (pp) cc_final: 0.8570 (pt) REVERT: M 6 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8176 (mt) REVERT: M 44 ARG cc_start: 0.7735 (tpp80) cc_final: 0.7457 (mmm-85) REVERT: N 15 LYS cc_start: 0.9013 (mttt) cc_final: 0.8665 (mttm) REVERT: O 1 MET cc_start: 0.4894 (ptp) cc_final: 0.4544 (mtp) REVERT: W 37 ASP cc_start: 0.6770 (m-30) cc_final: 0.6567 (m-30) REVERT: X 15 GLU cc_start: 0.6595 (pt0) cc_final: 0.6055 (mt-10) REVERT: X 84 LYS cc_start: 0.6975 (mmtp) cc_final: 0.6456 (ptpt) REVERT: Y 54 MET cc_start: 0.6465 (mtm) cc_final: 0.6244 (mtp) REVERT: Z 61 ASN cc_start: 0.7978 (m110) cc_final: 0.7727 (m110) REVERT: Z 89 ILE cc_start: 0.8689 (mm) cc_final: 0.8279 (mt) outliers start: 75 outliers final: 55 residues processed: 581 average time/residue: 0.8130 time to fit residues: 785.6944 Evaluate side-chains 537 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 481 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 51 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 399 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 480 optimal weight: 6.9990 chunk 518 optimal weight: 10.0000 chunk 427 optimal weight: 10.0000 chunk 476 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 385 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 57 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 ASN ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 104 ASN Y 12 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 83 GLN ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 86909 Z= 0.476 Angle : 0.817 11.458 130874 Z= 0.407 Chirality : 0.047 0.377 16863 Planarity : 0.007 0.070 6328 Dihedral : 24.199 179.796 45445 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 5.18 % Allowed : 13.64 % Favored : 81.17 % 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: -3.34 (0.14), residues: 2575 helix: -1.74 (0.19), residues: 632 sheet: -2.04 (0.21), residues: 504 loop : -2.57 (0.14), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 213 HIS 0.007 0.002 HIS E 102 PHE 0.037 0.003 PHE Z 86 TYR 0.029 0.003 TYR F 58 ARG 0.009 0.001 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 480 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7106 (mtm180) cc_final: 0.6715 (mtt180) REVERT: B 77 LYS cc_start: 0.7792 (tppt) cc_final: 0.7459 (tptp) REVERT: C 19 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8424 (mtpt) REVERT: C 114 LYS cc_start: 0.6743 (mttt) cc_final: 0.6494 (mttm) REVERT: D 18 GLN cc_start: 0.7779 (tt0) cc_final: 0.7524 (tt0) REVERT: E 90 GLN cc_start: 0.8349 (mt0) cc_final: 0.8109 (mt0) REVERT: F 14 GLU cc_start: 0.6363 (tt0) cc_final: 0.6039 (tp30) REVERT: F 65 MET cc_start: 0.4615 (ptm) cc_final: 0.4150 (mmm) REVERT: H 37 LYS cc_start: 0.5838 (ttpt) cc_final: 0.5617 (tttm) REVERT: I 84 LYS cc_start: 0.7977 (mttp) cc_final: 0.7639 (mtmm) REVERT: K 14 ILE cc_start: 0.7475 (mm) cc_final: 0.6910 (tt) REVERT: L 103 GLN cc_start: 0.6652 (OUTLIER) cc_final: 0.6106 (pm20) REVERT: M 6 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8175 (mt) REVERT: M 44 ARG cc_start: 0.7739 (tpp80) cc_final: 0.7445 (mmm-85) REVERT: M 47 ILE cc_start: 0.8449 (pt) cc_final: 0.8028 (mt) REVERT: N 15 LYS cc_start: 0.9022 (mttt) cc_final: 0.8625 (mttm) REVERT: O 1 MET cc_start: 0.4745 (ptp) cc_final: 0.4235 (mtp) REVERT: Q 28 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: S 40 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: W 37 ASP cc_start: 0.6732 (m-30) cc_final: 0.6526 (m-30) REVERT: X 15 GLU cc_start: 0.6721 (pt0) cc_final: 0.6250 (mt-10) REVERT: Y 54 MET cc_start: 0.6475 (mtm) cc_final: 0.6226 (mtp) REVERT: Z 16 MET cc_start: 0.7942 (tpp) cc_final: 0.7649 (tpp) REVERT: Z 89 ILE cc_start: 0.8814 (mm) cc_final: 0.8503 (mt) REVERT: a 99 TYR cc_start: 0.7080 (m-80) cc_final: 0.6880 (m-80) outliers start: 114 outliers final: 83 residues processed: 550 average time/residue: 0.9063 time to fit residues: 835.8527 Evaluate side-chains 555 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 467 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 190 ASP Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 51 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 4.9990 chunk 361 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 229 optimal weight: 0.9990 chunk 322 optimal weight: 4.9990 chunk 482 optimal weight: 10.0000 chunk 510 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 456 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN H 85 GLN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 182 ASN O 45 HIS V 3 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Z 83 GLN Z 106 GLN a 21 ASN ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 86909 Z= 0.410 Angle : 0.758 11.241 130874 Z= 0.380 Chirality : 0.044 0.357 16863 Planarity : 0.006 0.071 6328 Dihedral : 24.110 178.948 45445 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 5.68 % Allowed : 14.92 % Favored : 79.40 % 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: -3.12 (0.14), residues: 2575 helix: -1.58 (0.19), residues: 639 sheet: -1.84 (0.21), residues: 502 loop : -2.44 (0.14), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 213 HIS 0.006 0.001 HIS X 35 PHE 0.030 0.003 PHE Z 86 TYR 0.024 0.003 TYR a 101 ARG 0.007 0.001 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 486 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7025 (mtm180) cc_final: 0.6690 (mtt180) REVERT: B 77 LYS cc_start: 0.7804 (tppt) cc_final: 0.7460 (tptp) REVERT: B 171 TYR cc_start: 0.8254 (m-80) cc_final: 0.8020 (m-80) REVERT: C 19 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8449 (mtpt) REVERT: C 114 LYS cc_start: 0.6696 (mttt) cc_final: 0.6488 (mttm) REVERT: D 18 GLN cc_start: 0.7849 (tt0) cc_final: 0.7600 (tt0) REVERT: D 67 ARG cc_start: 0.8105 (mtm180) cc_final: 0.7573 (ptm160) REVERT: E 90 GLN cc_start: 0.8295 (mt0) cc_final: 0.8089 (mt0) REVERT: F 43 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6433 (mt-10) REVERT: F 65 MET cc_start: 0.4620 (ptm) cc_final: 0.4122 (mmm) REVERT: H 37 LYS cc_start: 0.5939 (ttpt) cc_final: 0.5706 (tttm) REVERT: H 42 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8083 (mtmm) REVERT: I 84 LYS cc_start: 0.7997 (mttp) cc_final: 0.7667 (mtmm) REVERT: J 27 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7254 (ppp80) REVERT: K 14 ILE cc_start: 0.7403 (mm) cc_final: 0.6849 (tt) REVERT: L 103 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.6081 (pm20) REVERT: L 162 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.6768 (ppt-90) REVERT: M 6 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8142 (mt) REVERT: M 44 ARG cc_start: 0.7681 (tpp80) cc_final: 0.7439 (mmm-85) REVERT: N 15 LYS cc_start: 0.8979 (mttt) cc_final: 0.8602 (mttm) REVERT: O 1 MET cc_start: 0.4736 (ptp) cc_final: 0.4220 (mtp) REVERT: S 21 ASP cc_start: 0.6644 (OUTLIER) cc_final: 0.6257 (t70) REVERT: S 40 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: X 15 GLU cc_start: 0.6741 (pt0) cc_final: 0.6306 (mt-10) REVERT: Y 83 MET cc_start: 0.8526 (mmp) cc_final: 0.7973 (mmp) REVERT: Z 89 ILE cc_start: 0.8808 (mm) cc_final: 0.8525 (mt) REVERT: a 82 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5860 (mppt) outliers start: 125 outliers final: 97 residues processed: 566 average time/residue: 0.8374 time to fit residues: 780.9869 Evaluate side-chains 578 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 472 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 190 ASP Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 9.9990 chunk 289 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 380 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 435 optimal weight: 7.9990 chunk 352 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 458 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 14 GLN A 43 GLN B 70 ASN B 226 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 3 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 86909 Z= 0.376 Angle : 0.730 10.766 130874 Z= 0.368 Chirality : 0.043 0.347 16863 Planarity : 0.006 0.070 6328 Dihedral : 24.065 179.166 45445 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 6.14 % Allowed : 16.05 % Favored : 77.81 % 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: -3.02 (0.14), residues: 2575 helix: -1.46 (0.19), residues: 644 sheet: -1.76 (0.21), residues: 501 loop : -2.40 (0.14), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 213 HIS 0.006 0.001 HIS X 35 PHE 0.027 0.002 PHE Z 86 TYR 0.025 0.003 TYR a 101 ARG 0.006 0.001 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 487 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.6968 (mtm180) cc_final: 0.6669 (mtt180) REVERT: B 77 LYS cc_start: 0.7794 (tppt) cc_final: 0.7459 (tptp) REVERT: C 19 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8384 (mtpt) REVERT: C 114 LYS cc_start: 0.6657 (mttt) cc_final: 0.6437 (mttm) REVERT: D 18 GLN cc_start: 0.7852 (tt0) cc_final: 0.7607 (tt0) REVERT: D 67 ARG cc_start: 0.8119 (mtm180) cc_final: 0.7576 (ptm160) REVERT: E 38 LEU cc_start: 0.8424 (mt) cc_final: 0.8017 (mt) REVERT: F 43 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6486 (mt-10) REVERT: F 65 MET cc_start: 0.4813 (ptm) cc_final: 0.4242 (mmm) REVERT: H 23 LYS cc_start: 0.7638 (mptp) cc_final: 0.7191 (tptt) REVERT: H 37 LYS cc_start: 0.5851 (ttpt) cc_final: 0.5609 (tttm) REVERT: H 42 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8081 (mtmm) REVERT: H 83 LYS cc_start: 0.6277 (mtmm) cc_final: 0.6032 (tttt) REVERT: I 84 LYS cc_start: 0.7998 (mttp) cc_final: 0.7675 (mtmm) REVERT: J 27 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7268 (ppp80) REVERT: K 14 ILE cc_start: 0.7385 (mm) cc_final: 0.6843 (tt) REVERT: L 103 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6052 (pm20) REVERT: L 104 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6611 (pm20) REVERT: L 162 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.6889 (ppt-90) REVERT: M 6 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8134 (mt) REVERT: M 44 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7472 (mmm-85) REVERT: N 15 LYS cc_start: 0.8960 (mttt) cc_final: 0.8586 (mttm) REVERT: N 22 ILE cc_start: 0.8094 (pt) cc_final: 0.7694 (pt) REVERT: O 1 MET cc_start: 0.4728 (ptp) cc_final: 0.4420 (mtp) REVERT: R 8 LYS cc_start: 0.8613 (ptpt) cc_final: 0.8335 (ptpt) REVERT: S 21 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6402 (t70) REVERT: S 40 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7133 (tt0) REVERT: W 87 ILE cc_start: 0.8807 (tt) cc_final: 0.8464 (pt) REVERT: X 15 GLU cc_start: 0.6679 (pt0) cc_final: 0.6198 (mt-10) REVERT: Y 83 MET cc_start: 0.8563 (mmp) cc_final: 0.8040 (mmp) REVERT: Z 89 ILE cc_start: 0.8806 (mm) cc_final: 0.8514 (mt) REVERT: a 82 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5830 (mppt) outliers start: 135 outliers final: 107 residues processed: 576 average time/residue: 0.8526 time to fit residues: 811.3340 Evaluate side-chains 590 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 473 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 190 ASP Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.0770 chunk 459 optimal weight: 10.0000 chunk 100 optimal weight: 0.4980 chunk 299 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 510 optimal weight: 6.9990 chunk 424 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 90 GLN H 85 GLN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 76 HIS L 128 GLN O 25 ASN O 40 ASN S 182 ASN V 3 GLN Y 12 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 86909 Z= 0.167 Angle : 0.594 9.987 130874 Z= 0.306 Chirality : 0.036 0.367 16863 Planarity : 0.004 0.067 6328 Dihedral : 23.953 179.031 45445 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.55 % Allowed : 18.28 % Favored : 77.17 % 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: -2.63 (0.15), residues: 2575 helix: -0.99 (0.20), residues: 630 sheet: -1.69 (0.21), residues: 519 loop : -2.15 (0.14), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 213 HIS 0.006 0.001 HIS C 29 PHE 0.020 0.002 PHE S 116 TYR 0.025 0.002 TYR a 101 ARG 0.005 0.000 ARG S 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 504 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7337 (ptm-80) cc_final: 0.6990 (ptm-80) REVERT: B 77 LYS cc_start: 0.7702 (tppt) cc_final: 0.7378 (tptp) REVERT: B 185 LEU cc_start: 0.8741 (tp) cc_final: 0.8440 (mp) REVERT: B 260 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.5363 (tmt90) REVERT: D 18 GLN cc_start: 0.7877 (tt0) cc_final: 0.7622 (tt0) REVERT: D 67 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7583 (ptm160) REVERT: E 38 LEU cc_start: 0.8373 (mt) cc_final: 0.8028 (mt) REVERT: F 43 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6381 (mt-10) REVERT: H 23 LYS cc_start: 0.7524 (mptp) cc_final: 0.7162 (tptt) REVERT: H 42 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7997 (mtmm) REVERT: I 84 LYS cc_start: 0.7969 (mttp) cc_final: 0.7613 (mtmm) REVERT: J 27 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7080 (ppp80) REVERT: K 14 ILE cc_start: 0.7322 (mm) cc_final: 0.6779 (tt) REVERT: L 103 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6159 (pm20) REVERT: L 162 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.6840 (ppt-90) REVERT: M 44 ARG cc_start: 0.7651 (tpp80) cc_final: 0.7377 (mmm-85) REVERT: N 15 LYS cc_start: 0.8907 (mttt) cc_final: 0.8569 (mttm) REVERT: O 1 MET cc_start: 0.4615 (ptp) cc_final: 0.4340 (mtp) REVERT: P 41 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8101 (ttpp) REVERT: S 40 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: W 87 ILE cc_start: 0.8745 (tt) cc_final: 0.8419 (pt) REVERT: X 15 GLU cc_start: 0.6418 (pt0) cc_final: 0.6095 (mt-10) REVERT: X 16 ARG cc_start: 0.8619 (ptp-170) cc_final: 0.8412 (ptm160) REVERT: Y 83 MET cc_start: 0.8600 (mmp) cc_final: 0.7996 (mmp) REVERT: Y 102 ILE cc_start: 0.8687 (mm) cc_final: 0.8483 (mm) REVERT: Z 89 ILE cc_start: 0.8757 (mm) cc_final: 0.8497 (mt) REVERT: a 82 LYS cc_start: 0.5745 (OUTLIER) cc_final: 0.5405 (mppt) outliers start: 100 outliers final: 75 residues processed: 568 average time/residue: 0.8516 time to fit residues: 796.6319 Evaluate side-chains 569 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 486 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 8.9990 chunk 57 optimal weight: 0.3980 chunk 291 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 430 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 508 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 chunk 310 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN V 3 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 12 GLN a 21 ASN ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 86909 Z= 0.545 Angle : 0.865 11.444 130874 Z= 0.425 Chirality : 0.049 0.389 16863 Planarity : 0.007 0.069 6328 Dihedral : 24.107 179.361 45445 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 6.46 % Allowed : 17.28 % Favored : 76.26 % 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: -2.88 (0.15), residues: 2575 helix: -1.38 (0.19), residues: 637 sheet: -1.66 (0.22), residues: 496 loop : -2.30 (0.14), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 213 HIS 0.007 0.002 HIS X 35 PHE 0.032 0.003 PHE Z 86 TYR 0.027 0.003 TYR a 101 ARG 0.011 0.001 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 474 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7033 (mtm180) cc_final: 0.6708 (mtt180) REVERT: B 77 LYS cc_start: 0.7823 (tppt) cc_final: 0.7482 (tptp) REVERT: B 260 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.5513 (tmt90) REVERT: C 19 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8343 (mtpt) REVERT: D 67 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7601 (ptm160) REVERT: E 38 LEU cc_start: 0.8452 (mt) cc_final: 0.8038 (mt) REVERT: F 43 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6504 (mt-10) REVERT: H 23 LYS cc_start: 0.7708 (mptp) cc_final: 0.7270 (tptt) REVERT: H 42 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8115 (mtmm) REVERT: J 27 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7358 (ppp80) REVERT: K 14 ILE cc_start: 0.7451 (mm) cc_final: 0.6888 (tt) REVERT: L 103 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.6060 (pm20) REVERT: L 104 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6600 (pm20) REVERT: L 162 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7110 (ppt-90) REVERT: N 15 LYS cc_start: 0.9047 (mttt) cc_final: 0.8639 (mttm) REVERT: S 40 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.6892 (tt0) REVERT: S 194 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7741 (tt) REVERT: W 5 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7492 (mm-30) REVERT: W 87 ILE cc_start: 0.8879 (tt) cc_final: 0.8520 (pt) REVERT: X 15 GLU cc_start: 0.6746 (pt0) cc_final: 0.6367 (mt-10) REVERT: Y 83 MET cc_start: 0.8565 (mmp) cc_final: 0.8057 (mmp) REVERT: Y 102 ILE cc_start: 0.8832 (mm) cc_final: 0.8573 (mm) REVERT: Y 134 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6143 (ttm170) REVERT: Z 89 ILE cc_start: 0.8742 (mm) cc_final: 0.8449 (mt) REVERT: a 82 LYS cc_start: 0.6451 (OUTLIER) cc_final: 0.5901 (mppt) outliers start: 142 outliers final: 111 residues processed: 571 average time/residue: 0.8442 time to fit residues: 798.0945 Evaluate side-chains 592 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 470 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 192 ASN Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 166 SER Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 190 ASP Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Y residue 134 ARG Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 303 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 346 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 400 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN H 85 GLN J 16 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN V 3 GLN X 81 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 97 GLN Z 106 GLN a 21 ASN ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 86909 Z= 0.171 Angle : 0.585 9.943 130874 Z= 0.303 Chirality : 0.036 0.382 16863 Planarity : 0.004 0.066 6328 Dihedral : 23.886 179.878 45445 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.64 % Allowed : 19.87 % Favored : 75.49 % 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: -2.48 (0.15), residues: 2575 helix: -0.91 (0.20), residues: 630 sheet: -1.53 (0.22), residues: 512 loop : -2.06 (0.14), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 213 HIS 0.005 0.001 HIS C 29 PHE 0.017 0.001 PHE Z 86 TYR 0.026 0.002 TYR a 101 ARG 0.006 0.000 ARG X 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 498 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7404 (ptm-80) cc_final: 0.7021 (ptm-80) REVERT: A 111 ARG cc_start: 0.6935 (mtm180) cc_final: 0.6664 (mtt180) REVERT: B 77 LYS cc_start: 0.7764 (tppt) cc_final: 0.7438 (tptp) REVERT: B 180 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6968 (tp30) REVERT: B 260 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.5457 (tmt90) REVERT: C 19 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8172 (mtpt) REVERT: D 18 GLN cc_start: 0.7854 (tt0) cc_final: 0.7603 (tt0) REVERT: D 67 ARG cc_start: 0.8031 (mtm180) cc_final: 0.7559 (ptm160) REVERT: E 38 LEU cc_start: 0.8362 (mt) cc_final: 0.8016 (mt) REVERT: F 43 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6414 (mt-10) REVERT: H 23 LYS cc_start: 0.7546 (mptp) cc_final: 0.7167 (tptt) REVERT: H 42 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8001 (mtmm) REVERT: I 84 LYS cc_start: 0.7960 (mttp) cc_final: 0.7597 (mtmm) REVERT: J 27 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7039 (ppp80) REVERT: K 14 ILE cc_start: 0.7344 (mm) cc_final: 0.6792 (tt) REVERT: L 162 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.6852 (ppt-90) REVERT: N 15 LYS cc_start: 0.8917 (mttt) cc_final: 0.8562 (mttm) REVERT: P 41 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8102 (ttpp) REVERT: Q 55 MET cc_start: 0.7350 (mmm) cc_final: 0.7137 (mmm) REVERT: S 40 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.6818 (tt0) REVERT: V 14 ARG cc_start: 0.8489 (mtt90) cc_final: 0.8265 (mtt90) REVERT: W 87 ILE cc_start: 0.8749 (tt) cc_final: 0.8421 (pt) REVERT: X 15 GLU cc_start: 0.6586 (pt0) cc_final: 0.6376 (mt-10) REVERT: Y 83 MET cc_start: 0.8592 (mmp) cc_final: 0.7976 (mmp) REVERT: Z 89 ILE cc_start: 0.8662 (mm) cc_final: 0.8431 (mt) REVERT: a 82 LYS cc_start: 0.5839 (OUTLIER) cc_final: 0.5479 (mppt) outliers start: 102 outliers final: 83 residues processed: 565 average time/residue: 0.8418 time to fit residues: 783.9812 Evaluate side-chains 575 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 483 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 73 GLU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 10.0000 chunk 487 optimal weight: 7.9990 chunk 444 optimal weight: 6.9990 chunk 474 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 chunk 206 optimal weight: 0.0770 chunk 372 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 428 optimal weight: 10.0000 chunk 448 optimal weight: 8.9990 chunk 472 optimal weight: 8.9990 overall best weight: 6.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN J 16 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN S 141 ASN V 3 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 97 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 86909 Z= 0.557 Angle : 0.884 11.432 130874 Z= 0.434 Chirality : 0.050 0.390 16863 Planarity : 0.007 0.068 6328 Dihedral : 24.106 179.373 45445 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 5.73 % Allowed : 18.64 % Favored : 75.63 % 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: -2.79 (0.15), residues: 2575 helix: -1.29 (0.19), residues: 631 sheet: -1.63 (0.21), residues: 507 loop : -2.23 (0.14), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 213 HIS 0.007 0.002 HIS Q 31 PHE 0.032 0.003 PHE Z 86 TYR 0.030 0.003 TYR a 101 ARG 0.012 0.001 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 481 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.6986 (mtm180) cc_final: 0.6672 (mtt180) REVERT: B 77 LYS cc_start: 0.7867 (tppt) cc_final: 0.7511 (tptp) REVERT: B 180 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7064 (tp30) REVERT: B 260 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.5486 (tmt90) REVERT: C 19 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8354 (mtpt) REVERT: D 67 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7610 (ptm160) REVERT: H 23 LYS cc_start: 0.7686 (mptp) cc_final: 0.7271 (tptt) REVERT: I 84 LYS cc_start: 0.8018 (mttp) cc_final: 0.7671 (mtmm) REVERT: J 27 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7428 (ppp80) REVERT: K 14 ILE cc_start: 0.7457 (mm) cc_final: 0.6892 (tt) REVERT: L 104 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6869 (pm20) REVERT: L 162 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7200 (ppt-90) REVERT: N 15 LYS cc_start: 0.9051 (mttt) cc_final: 0.8641 (mttm) REVERT: S 40 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: W 5 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7536 (mm-30) REVERT: W 87 ILE cc_start: 0.8895 (tt) cc_final: 0.8543 (pt) REVERT: X 15 GLU cc_start: 0.6829 (pt0) cc_final: 0.6548 (mt-10) REVERT: Y 83 MET cc_start: 0.8559 (mmp) cc_final: 0.8040 (mmp) REVERT: Y 134 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6055 (ttm170) REVERT: Z 89 ILE cc_start: 0.8733 (mm) cc_final: 0.8447 (mt) REVERT: a 82 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.5890 (mppt) outliers start: 126 outliers final: 106 residues processed: 566 average time/residue: 0.8669 time to fit residues: 813.6165 Evaluate side-chains 590 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 475 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 12 CYS Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 190 ASP Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 41 CYS Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 73 GLU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Y residue 134 ARG Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 2.9990 chunk 501 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 chunk 237 optimal weight: 0.8980 chunk 348 optimal weight: 3.9990 chunk 526 optimal weight: 9.9990 chunk 484 optimal weight: 5.9990 chunk 418 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 323 optimal weight: 0.9990 chunk 256 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN G 39 ASN H 85 GLN L 37 GLN M 40 ASN V 3 GLN X 81 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN a 21 ASN ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 86909 Z= 0.162 Angle : 0.576 9.933 130874 Z= 0.298 Chirality : 0.036 0.391 16863 Planarity : 0.004 0.065 6328 Dihedral : 23.816 179.842 45445 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.27 % Allowed : 20.46 % Favored : 75.26 % 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: -2.36 (0.15), residues: 2575 helix: -0.77 (0.20), residues: 625 sheet: -1.43 (0.22), residues: 512 loop : -2.01 (0.14), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 213 HIS 0.008 0.001 HIS E 60 PHE 0.017 0.001 PHE Z 86 TYR 0.026 0.001 TYR a 101 ARG 0.006 0.000 ARG X 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 505 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7359 (ptm-80) cc_final: 0.6952 (ptm-80) REVERT: A 111 ARG cc_start: 0.6931 (mtm180) cc_final: 0.6657 (mtt180) REVERT: B 77 LYS cc_start: 0.7763 (tppt) cc_final: 0.7417 (tptp) REVERT: B 180 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6927 (tp30) REVERT: B 260 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.5438 (tmt90) REVERT: C 19 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8136 (mtpt) REVERT: D 1 MET cc_start: 0.6119 (tpt) cc_final: 0.4729 (tpt) REVERT: D 18 GLN cc_start: 0.7766 (tt0) cc_final: 0.7520 (tt0) REVERT: D 67 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7531 (ptm160) REVERT: E 37 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7533 (mtpp) REVERT: E 38 LEU cc_start: 0.8341 (mt) cc_final: 0.8019 (mt) REVERT: F 43 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6432 (mt-10) REVERT: F 65 MET cc_start: 0.4273 (tmm) cc_final: 0.4013 (tmm) REVERT: H 23 LYS cc_start: 0.7524 (mptp) cc_final: 0.7179 (tptt) REVERT: I 84 LYS cc_start: 0.7916 (mttp) cc_final: 0.7603 (mtmm) REVERT: J 27 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7085 (ppp80) REVERT: K 14 ILE cc_start: 0.7430 (mm) cc_final: 0.6769 (tt) REVERT: L 78 LYS cc_start: 0.7283 (mmmt) cc_final: 0.7075 (tppt) REVERT: L 162 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.6521 (ppt-90) REVERT: N 15 LYS cc_start: 0.8912 (mttt) cc_final: 0.8566 (mttm) REVERT: P 41 LYS cc_start: 0.8353 (ttpt) cc_final: 0.8094 (ttpp) REVERT: S 40 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: S 116 PHE cc_start: 0.8056 (t80) cc_final: 0.7729 (t80) REVERT: V 14 ARG cc_start: 0.8482 (mtt90) cc_final: 0.8141 (mtt90) REVERT: W 5 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7503 (mm-30) REVERT: W 87 ILE cc_start: 0.8752 (tt) cc_final: 0.8414 (pt) REVERT: X 18 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7718 (mtp180) REVERT: Z 89 ILE cc_start: 0.8609 (mm) cc_final: 0.8389 (mt) REVERT: a 82 LYS cc_start: 0.5796 (OUTLIER) cc_final: 0.5457 (mppt) outliers start: 94 outliers final: 75 residues processed: 570 average time/residue: 0.8535 time to fit residues: 803.0799 Evaluate side-chains 576 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 493 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 190 ASP Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 18 ARG Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 6.9990 chunk 446 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 386 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 419 optimal weight: 7.9990 chunk 175 optimal weight: 0.8980 chunk 430 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN G 39 ASN L 33 ASN L 37 GLN L 181 GLN V 3 GLN X 81 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.122204 restraints weight = 104585.083| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 0.59 r_work: 0.3050 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 86909 Z= 0.244 Angle : 0.614 9.871 130874 Z= 0.314 Chirality : 0.037 0.365 16863 Planarity : 0.005 0.067 6328 Dihedral : 23.801 178.951 45445 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.77 % Allowed : 20.19 % Favored : 75.03 % 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: -2.28 (0.15), residues: 2575 helix: -0.73 (0.20), residues: 625 sheet: -1.34 (0.22), residues: 507 loop : -1.97 (0.14), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 213 HIS 0.005 0.001 HIS C 29 PHE 0.018 0.002 PHE Z 86 TYR 0.027 0.002 TYR a 101 ARG 0.006 0.000 ARG X 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14415.13 seconds wall clock time: 256 minutes 50.16 seconds (15410.16 seconds total)