Starting phenix.real_space_refine on Tue Nov 19 03:42:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/11_2024/8s9s_40245.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/11_2024/8s9s_40245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/11_2024/8s9s_40245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/11_2024/8s9s_40245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/11_2024/8s9s_40245.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/11_2024/8s9s_40245.cif" } resolution = 3.6 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= 0.003 sd= 0.014 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 72 5.16 5 C 11530 2.51 5 N 3066 2.21 5 O 3338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18012 Number of models: 1 Model: "" Number of chains: 15 Chain: "1" Number of atoms: 7367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7367 Classifications: {'peptide': 930} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 886} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "2" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2306 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 276} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1833 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "4" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 867 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 10, 'TRANS': 133} Chain breaks: 2 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "5" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 795 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 97} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "6" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 774 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "7" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1054 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 124} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "8" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1533 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 8, 'TRANS': 183} Chain breaks: 1 Chain: "10" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1177 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 145} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "3" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 8 Chain: "6" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 11.19, per 1000 atoms: 0.62 Number of scatterers: 18012 At special positions: 0 Unit cell: (93.184, 123.968, 210.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 6 15.00 O 3338 8.00 N 3066 7.00 C 11530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 1 227 " - pdb=" SG CYS 1 237 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 338 " - pdb=" SG CYS 1 368 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG 11001 " - " ASN 1 370 " " NAG A 1 " - " ASN 1 913 " " NAG B 1 " - " ASN 1 818 " " NAG C 1 " - " ASN10 182 " Time building additional restraints: 4.57 Conformation dependent library (CDL) restraints added in 2.6 seconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 26 sheets defined 40.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain '1' and resid 82 through 85 removed outlier: 3.689A pdb=" N GLY 1 85 " --> pdb=" O THR 1 82 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 82 through 85' Processing helix chain '1' and resid 222 through 227 removed outlier: 3.884A pdb=" N ALA 1 226 " --> pdb=" O HIS 1 222 " (cutoff:3.500A) Processing helix chain '1' and resid 261 through 265 Processing helix chain '1' and resid 446 through 450 Processing helix chain '1' and resid 463 through 468 removed outlier: 4.555A pdb=" N GLU 1 468 " --> pdb=" O GLY 1 464 " (cutoff:3.500A) Processing helix chain '1' and resid 469 through 471 No H-bonds generated for 'chain '1' and resid 469 through 471' Processing helix chain '1' and resid 479 through 500 removed outlier: 3.565A pdb=" N MET 1 483 " --> pdb=" O GLY 1 479 " (cutoff:3.500A) Processing helix chain '1' and resid 655 through 665 Processing helix chain '1' and resid 876 through 879 removed outlier: 3.578A pdb=" N ASP 1 879 " --> pdb=" O ALA 1 876 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 876 through 879' Processing helix chain '1' and resid 887 through 894 Processing helix chain '1' and resid 905 through 909 removed outlier: 3.628A pdb=" N PHE 1 909 " --> pdb=" O ALA 1 906 " (cutoff:3.500A) Processing helix chain '1' and resid 961 through 993 removed outlier: 3.824A pdb=" N SER 1 967 " --> pdb=" O VAL 1 963 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE 1 974 " --> pdb=" O PHE 1 970 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA 1 975 " --> pdb=" O GLY 1 971 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 25 Processing helix chain '2' and resid 29 through 44 Processing helix chain '2' and resid 50 through 67 removed outlier: 4.242A pdb=" N ILE 2 54 " --> pdb=" O ASP 2 50 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE 2 55 " --> pdb=" O ASP 2 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET 2 60 " --> pdb=" O TYR 2 56 " (cutoff:3.500A) Processing helix chain '2' and resid 69 through 83 removed outlier: 3.602A pdb=" N LEU 2 73 " --> pdb=" O ASP 2 69 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE 2 74 " --> pdb=" O ASP 2 70 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 99 Processing helix chain '2' and resid 102 through 117 removed outlier: 3.854A pdb=" N ALA 2 106 " --> pdb=" O ARG 2 102 " (cutoff:3.500A) Processing helix chain '2' and resid 121 through 134 Processing helix chain '2' and resid 136 through 149 Processing helix chain '2' and resid 154 through 169 Processing helix chain '2' and resid 170 through 185 Processing helix chain '2' and resid 188 through 203 removed outlier: 3.683A pdb=" N CYS 2 192 " --> pdb=" O ASN 2 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY 2 203 " --> pdb=" O LYS 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 204 through 222 removed outlier: 4.554A pdb=" N LEU 2 210 " --> pdb=" O GLU 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 242 Processing helix chain '2' and resid 246 through 275 removed outlier: 3.514A pdb=" N LYS 2 275 " --> pdb=" O ALA 2 271 " (cutoff:3.500A) Processing helix chain '2' and resid 279 through 290 removed outlier: 3.500A pdb=" N GLU 2 290 " --> pdb=" O GLU 2 286 " (cutoff:3.500A) Processing helix chain '3' and resid 10 through 17 removed outlier: 3.722A pdb=" N LEU 3 14 " --> pdb=" O SER 3 10 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 39 Processing helix chain '3' and resid 45 through 65 removed outlier: 3.541A pdb=" N VAL 3 49 " --> pdb=" O THR 3 45 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 68 No H-bonds generated for 'chain '3' and resid 66 through 68' Processing helix chain '3' and resid 69 through 81 Processing helix chain '3' and resid 104 through 116 Processing helix chain '3' and resid 118 through 132 Processing helix chain '3' and resid 145 through 147 No H-bonds generated for 'chain '3' and resid 145 through 147' Processing helix chain '3' and resid 148 through 153 Processing helix chain '3' and resid 167 through 178 Processing helix chain '3' and resid 179 through 187 Processing helix chain '3' and resid 214 through 228 Processing helix chain '3' and resid 232 through 235 Processing helix chain '3' and resid 236 through 243 removed outlier: 3.581A pdb=" N ALA 3 243 " --> pdb=" O GLU 3 239 " (cutoff:3.500A) Processing helix chain '4' and resid 67 through 91 removed outlier: 3.528A pdb=" N ASP 4 71 " --> pdb=" O LYS 4 67 " (cutoff:3.500A) Proline residue: 4 76 - end of helix Proline residue: 4 81 - end of helix removed outlier: 3.960A pdb=" N GLY 4 91 " --> pdb=" O MET 4 87 " (cutoff:3.500A) Processing helix chain '4' and resid 91 through 96 Processing helix chain '4' and resid 97 through 108 removed outlier: 3.875A pdb=" N VAL 4 102 " --> pdb=" O PRO 4 98 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG 4 108 " --> pdb=" O MET 4 104 " (cutoff:3.500A) Processing helix chain '4' and resid 110 through 115 Processing helix chain '4' and resid 115 through 123 Processing helix chain '4' and resid 127 through 155 removed outlier: 4.011A pdb=" N LEU 4 131 " --> pdb=" O SER 4 127 " (cutoff:3.500A) Processing helix chain '4' and resid 161 through 168 removed outlier: 4.697A pdb=" N ALA 4 166 " --> pdb=" O ASP 4 163 " (cutoff:3.500A) Processing helix chain '5' and resid 4 through 35 removed outlier: 3.596A pdb=" N GLY 5 8 " --> pdb=" O SER 5 4 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 64 removed outlier: 3.547A pdb=" N HIS 5 62 " --> pdb=" O TYR 5 58 " (cutoff:3.500A) Processing helix chain '5' and resid 80 through 85 removed outlier: 3.846A pdb=" N LEU 5 84 " --> pdb=" O THR 5 80 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG 5 85 " --> pdb=" O PHE 5 81 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 80 through 85' Processing helix chain '5' and resid 87 through 91 removed outlier: 3.654A pdb=" N TYR 5 91 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) Processing helix chain '5' and resid 95 through 101 removed outlier: 4.285A pdb=" N VAL 5 99 " --> pdb=" O HIS 5 95 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 45 Processing helix chain '6' and resid 48 through 71 Processing helix chain '6' and resid 73 through 77 removed outlier: 3.615A pdb=" N LYS 6 76 " --> pdb=" O ARG 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 81 through 87 removed outlier: 3.590A pdb=" N PHE 6 85 " --> pdb=" O ARG 6 81 " (cutoff:3.500A) Processing helix chain '6' and resid 88 through 108 removed outlier: 3.586A pdb=" N THR 6 95 " --> pdb=" O GLY 6 91 " (cutoff:3.500A) Processing helix chain '7' and resid 57 through 62 removed outlier: 4.015A pdb=" N TRP 7 61 " --> pdb=" O LYS 7 57 " (cutoff:3.500A) Processing helix chain '7' and resid 156 through 162 removed outlier: 4.215A pdb=" N MET 7 162 " --> pdb=" O THR 7 158 " (cutoff:3.500A) Processing helix chain '7' and resid 163 through 178 Proline residue: 7 172 - end of helix Processing helix chain '8' and resid 7 through 21 removed outlier: 3.543A pdb=" N TYR 8 21 " --> pdb=" O HIS 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 67 through 85 removed outlier: 4.018A pdb=" N LEU 8 71 " --> pdb=" O LEU 8 67 " (cutoff:3.500A) Processing helix chain '8' and resid 105 through 117 Processing helix chain '8' and resid 129 through 132 Processing helix chain '8' and resid 163 through 177 Processing helix chain '8' and resid 185 through 192 Processing helix chain '8' and resid 199 through 210 removed outlier: 3.904A pdb=" N ASN 8 203 " --> pdb=" O ASN 8 199 " (cutoff:3.500A) Processing helix chain '10' and resid 91 through 104 Processing helix chain '10' and resid 134 through 139 Processing helix chain '10' and resid 174 through 180 removed outlier: 3.626A pdb=" N GLU10 179 " --> pdb=" O VAL10 176 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU10 180 " --> pdb=" O ASP10 177 " (cutoff:3.500A) Processing helix chain '10' and resid 198 through 210 Processing sheet with id=AA1, first strand: chain '1' and resid 32 through 34 Processing sheet with id=AA2, first strand: chain '1' and resid 42 through 44 removed outlier: 7.018A pdb=" N ILE 1 63 " --> pdb=" O ARG 1 76 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG 1 76 " --> pdb=" O ILE 1 63 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA 1 65 " --> pdb=" O LEU 1 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 87 through 93 removed outlier: 6.886A pdb=" N VAL 1 100 " --> pdb=" O ASP 1 88 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N MET 1 90 " --> pdb=" O ILE 1 98 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE 1 98 " --> pdb=" O MET 1 90 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU 1 92 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP 1 96 " --> pdb=" O LEU 1 92 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N MET 1 107 " --> pdb=" O GLU 1 120 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU 1 120 " --> pdb=" O MET 1 107 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER 1 109 " --> pdb=" O ASN 1 118 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY 1 116 " --> pdb=" O GLU 1 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 128 through 135 removed outlier: 7.133A pdb=" N LEU 1 146 " --> pdb=" O GLN 1 129 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEU 1 131 " --> pdb=" O ALA 1 144 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA 1 144 " --> pdb=" O LEU 1 131 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU 1 133 " --> pdb=" O TYR 1 142 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TYR 1 142 " --> pdb=" O LEU 1 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY 1 135 " --> pdb=" O VAL 1 140 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL 1 140 " --> pdb=" O GLY 1 135 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU 1 151 " --> pdb=" O VAL 1 164 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL 1 164 " --> pdb=" O LEU 1 151 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU 1 153 " --> pdb=" O LYS 1 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 174 through 181 removed outlier: 5.162A pdb=" N TYR 1 175 " --> pdb=" O VAL 1 191 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL 1 191 " --> pdb=" O TYR 1 175 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET 1 177 " --> pdb=" O LEU 1 189 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR 1 181 " --> pdb=" O VAL 1 185 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL 1 185 " --> pdb=" O TYR 1 181 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN 1 203 " --> pdb=" O ILE 1 209 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE 1 209 " --> pdb=" O ASN 1 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 228 through 230 Processing sheet with id=AA7, first strand: chain '1' and resid 275 through 277 removed outlier: 6.844A pdb=" N TYR 1 300 " --> pdb=" O ASN 1 315 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN 1 315 " --> pdb=" O TYR 1 300 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU 1 302 " --> pdb=" O LEU 1 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 322 through 326 Processing sheet with id=AA9, first strand: chain '1' and resid 402 through 411 removed outlier: 6.553A pdb=" N GLN 1 424 " --> pdb=" O GLU 1 403 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU 1 405 " --> pdb=" O LEU 1 422 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU 1 422 " --> pdb=" O LEU 1 405 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE 1 407 " --> pdb=" O ARG 1 420 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG 1 420 " --> pdb=" O ILE 1 407 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL 1 409 " --> pdb=" O GLY 1 418 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY 1 418 " --> pdb=" O VAL 1 409 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU 1 430 " --> pdb=" O SER 1 444 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER 1 444 " --> pdb=" O LEU 1 430 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE 1 432 " --> pdb=" O LEU 1 442 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '1' and resid 452 through 458 removed outlier: 3.616A pdb=" N CYS 1 454 " --> pdb=" O VAL 1 539 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU 1 545 " --> pdb=" O LYS 1 558 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS 1 558 " --> pdb=" O LEU 1 545 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY 1 547 " --> pdb=" O LEU 1 556 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1' and resid 572 through 576 removed outlier: 6.454A pdb=" N GLN 1 586 " --> pdb=" O GLN 1 575 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '1' and resid 623 through 632 removed outlier: 6.767A pdb=" N ILE 1 643 " --> pdb=" O LEU 1 624 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER 1 626 " --> pdb=" O LEU 1 641 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU 1 641 " --> pdb=" O SER 1 626 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU 1 628 " --> pdb=" O VAL 1 639 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL 1 639 " --> pdb=" O LEU 1 628 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '1' and resid 694 through 699 Processing sheet with id=AB5, first strand: chain '1' and resid 705 through 709 removed outlier: 5.661A pdb=" N ILE 1 707 " --> pdb=" O GLU 1 746 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU 1 746 " --> pdb=" O ILE 1 707 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE 1 756 " --> pdb=" O SER 1 747 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS 1 771 " --> pdb=" O LEU 1 761 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '1' and resid 723 through 727 removed outlier: 5.417A pdb=" N VAL 1 725 " --> pdb=" O LEU 1 732 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU 1 732 " --> pdb=" O VAL 1 725 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY 1 727 " --> pdb=" O SER 1 730 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '1' and resid 779 through 786 removed outlier: 4.451A pdb=" N TRP 1 796 " --> pdb=" O PRO 1 781 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '1' and resid 779 through 786 removed outlier: 4.451A pdb=" N TRP 1 796 " --> pdb=" O PRO 1 781 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '1' and resid 821 through 822 Processing sheet with id=AC1, first strand: chain '1' and resid 860 through 864 Processing sheet with id=AC2, first strand: chain '3' and resid 138 through 139 removed outlier: 3.888A pdb=" N THR 3 138 " --> pdb=" O VAL 3 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '7' and resid 84 through 89 removed outlier: 5.268A pdb=" N VAL 7 85 " --> pdb=" O GLY 7 49 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLY 7 49 " --> pdb=" O VAL 7 85 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N HIS 7 87 " --> pdb=" O ILE 7 47 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE 7 47 " --> pdb=" O HIS 7 87 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU 7 138 " --> pdb=" O GLU 7 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '7' and resid 74 through 77 removed outlier: 4.047A pdb=" N ALA 7 120 " --> pdb=" O LEU 7 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '8' and resid 4 through 6 removed outlier: 7.465A pdb=" N LYS 8 5 " --> pdb=" O PHE 8 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '8' and resid 56 through 62 removed outlier: 3.902A pdb=" N ASN 8 27 " --> pdb=" O LEU 8 60 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL 8 26 " --> pdb=" O GLN 8 94 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLN 8 94 " --> pdb=" O VAL 8 26 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY 8 28 " --> pdb=" O TYR 8 92 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR 8 92 " --> pdb=" O GLY 8 28 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU 8 30 " --> pdb=" O ALA 8 90 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N ALA 8 123 " --> pdb=" O VAL 8 88 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA 8 90 " --> pdb=" O ALA 8 123 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE 8 125 " --> pdb=" O ALA 8 90 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR 8 92 " --> pdb=" O ILE 8 125 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL 8 127 " --> pdb=" O TYR 8 92 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLN 8 94 " --> pdb=" O VAL 8 127 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '10' and resid 82 through 87 removed outlier: 3.501A pdb=" N SER10 84 " --> pdb=" O LEU10 75 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS10 70 " --> pdb=" O HIS10 58 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS10 58 " --> pdb=" O LYS10 70 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU10 55 " --> pdb=" O PRO10 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '10' and resid 156 through 163 removed outlier: 3.515A pdb=" N VAL10 150 " --> pdb=" O GLN10 188 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2409 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.88 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2927 1.31 - 1.44: 4967 1.44 - 1.57: 10376 1.57 - 1.70: 13 1.70 - 1.83: 121 Bond restraints: 18404 Sorted by residual: bond pdb=" C11 PCW 3 303 " pdb=" O3 PCW 3 303 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C11 PCW 6 202 " pdb=" O3 PCW 6 202 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C11 PCW 3 302 " pdb=" O3 PCW 3 302 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C11 PCW 3 301 " pdb=" O3 PCW 3 301 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C11 PCW 11002 " pdb=" O3 PCW 11002 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.14e+01 ... (remaining 18399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.05: 24858 5.05 - 10.11: 78 10.11 - 15.16: 16 15.16 - 20.21: 2 20.21 - 25.27: 1 Bond angle restraints: 24955 Sorted by residual: angle pdb=" CA PRO 3 83 " pdb=" N PRO 3 83 " pdb=" CD PRO 3 83 " ideal model delta sigma weight residual 112.00 97.73 14.27 1.40e+00 5.10e-01 1.04e+02 angle pdb=" C19 PCW 3 302 " pdb=" C20 PCW 3 302 " pdb=" C21 PCW 3 302 " ideal model delta sigma weight residual 127.82 153.09 -25.27 3.00e+00 1.11e-01 7.09e+01 angle pdb=" O PRO 4 76 " pdb=" C PRO 4 76 " pdb=" N LEU 4 77 " ideal model delta sigma weight residual 122.22 115.09 7.13 1.29e+00 6.01e-01 3.05e+01 angle pdb=" C18 PCW 3 301 " pdb=" C19 PCW 3 301 " pdb=" C20 PCW 3 301 " ideal model delta sigma weight residual 127.82 112.22 15.60 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C18 PCW 3 302 " pdb=" C19 PCW 3 302 " pdb=" C20 PCW 3 302 " ideal model delta sigma weight residual 127.82 112.55 15.27 3.00e+00 1.11e-01 2.59e+01 ... (remaining 24950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 10639 35.12 - 70.23: 424 70.23 - 105.35: 38 105.35 - 140.47: 1 140.47 - 175.58: 7 Dihedral angle restraints: 11109 sinusoidal: 4534 harmonic: 6575 Sorted by residual: dihedral pdb=" N PCW 11002 " pdb=" C4 PCW 11002 " pdb=" C5 PCW 11002 " pdb=" O4P PCW 11002 " ideal model delta sinusoidal sigma weight residual -66.66 108.92 -175.58 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N PCW 6 202 " pdb=" C4 PCW 6 202 " pdb=" C5 PCW 6 202 " pdb=" O4P PCW 6 202 " ideal model delta sinusoidal sigma weight residual 293.34 132.79 160.55 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C2 PCW 3 303 " pdb=" C31 PCW 3 303 " pdb=" O2 PCW 3 303 " pdb=" C32 PCW 3 303 " ideal model delta sinusoidal sigma weight residual 175.43 16.62 158.81 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 11106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2257 0.050 - 0.100: 459 0.100 - 0.150: 80 0.150 - 0.200: 3 0.200 - 0.250: 6 Chirality restraints: 2805 Sorted by residual: chirality pdb=" C2 PCW 11002 " pdb=" C1 PCW 11002 " pdb=" C3 PCW 11002 " pdb=" O2 PCW 11002 " both_signs ideal model delta sigma weight residual False -2.32 -2.57 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C2 PCW 3 303 " pdb=" C1 PCW 3 303 " pdb=" C3 PCW 3 303 " pdb=" O2 PCW 3 303 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C2 PCW 3 301 " pdb=" C1 PCW 3 301 " pdb=" C3 PCW 3 301 " pdb=" O2 PCW 3 301 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2802 not shown) Planarity restraints: 3168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO 4 76 " 0.043 2.00e-02 2.50e+03 8.11e-02 6.58e+01 pdb=" C PRO 4 76 " -0.140 2.00e-02 2.50e+03 pdb=" O PRO 4 76 " 0.052 2.00e-02 2.50e+03 pdb=" N LEU 4 77 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO 4 98 " 0.029 2.00e-02 2.50e+03 5.60e-02 3.13e+01 pdb=" C PRO 4 98 " -0.097 2.00e-02 2.50e+03 pdb=" O PRO 4 98 " 0.036 2.00e-02 2.50e+03 pdb=" N THR 4 99 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN 3 82 " -0.094 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO 3 83 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO 3 83 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO 3 83 " -0.069 5.00e-02 4.00e+02 ... (remaining 3165 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 975 2.73 - 3.27: 18569 3.27 - 3.81: 30555 3.81 - 4.36: 34523 4.36 - 4.90: 59690 Nonbonded interactions: 144312 Sorted by model distance: nonbonded pdb=" OG SER10 140 " pdb=" OG SER10 143 " model vdw 2.184 3.040 nonbonded pdb=" O ALA 5 52 " pdb=" OG1 THR 5 56 " model vdw 2.195 3.040 nonbonded pdb=" O THR 3 137 " pdb=" OH TYR 6 110 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP 5 82 " pdb=" NE2 HIS 8 62 " model vdw 2.205 3.120 nonbonded pdb=" OE2 GLU10 61 " pdb=" ND2 ASN10 67 " model vdw 2.221 3.120 ... (remaining 144307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 42.460 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 18404 Z= 0.339 Angle : 0.824 25.267 24955 Z= 0.383 Chirality : 0.043 0.250 2805 Planarity : 0.005 0.131 3164 Dihedral : 18.618 175.582 6855 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.59 % Allowed : 28.32 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2228 helix: 1.19 (0.19), residues: 784 sheet: -0.32 (0.24), residues: 492 loop : -0.71 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP 2 158 HIS 0.003 0.001 HIS 2 187 PHE 0.016 0.001 PHE 2 230 TYR 0.021 0.001 TYR 1 912 ARG 0.008 0.000 ARG 7 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 726 MET cc_start: 0.7853 (tpp) cc_final: 0.7587 (tpp) REVERT: 2 19 MET cc_start: 0.9416 (mmm) cc_final: 0.9194 (mmm) REVERT: 2 183 MET cc_start: 0.8860 (mtp) cc_final: 0.8467 (mtt) REVERT: 2 254 MET cc_start: 0.9200 (mtp) cc_final: 0.8815 (mmm) REVERT: 3 251 MET cc_start: 0.8701 (tpp) cc_final: 0.7833 (tmm) outliers start: 11 outliers final: 6 residues processed: 121 average time/residue: 0.3009 time to fit residues: 58.4668 Evaluate side-chains 98 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 2 residue 230 PHE Chi-restraints excluded: chain 8 residue 195 ASN Chi-restraints excluded: chain 8 residue 204 LYS Chi-restraints excluded: chain 10 residue 173 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 202 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18404 Z= 0.197 Angle : 0.584 8.212 24955 Z= 0.298 Chirality : 0.041 0.189 2805 Planarity : 0.004 0.063 3164 Dihedral : 12.439 166.795 2771 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.43 % Allowed : 25.21 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2228 helix: 1.71 (0.19), residues: 794 sheet: -0.27 (0.24), residues: 514 loop : -0.61 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 2 158 HIS 0.003 0.001 HIS10 58 PHE 0.022 0.001 PHE 2 230 TYR 0.013 0.001 TYR 1 672 ARG 0.005 0.000 ARG 2 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 96 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 726 MET cc_start: 0.7950 (tpp) cc_final: 0.7345 (tpp) REVERT: 2 183 MET cc_start: 0.8818 (mtp) cc_final: 0.8451 (mtt) REVERT: 2 226 MET cc_start: 0.7842 (ppp) cc_final: 0.7458 (ppp) REVERT: 2 254 MET cc_start: 0.9240 (mtp) cc_final: 0.8838 (mmm) REVERT: 3 251 MET cc_start: 0.8680 (tpp) cc_final: 0.7831 (tmm) REVERT: 8 71 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9410 (pp) REVERT: 8 85 HIS cc_start: 0.9313 (OUTLIER) cc_final: 0.9092 (m90) outliers start: 64 outliers final: 30 residues processed: 153 average time/residue: 0.2866 time to fit residues: 72.8343 Evaluate side-chains 125 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 452 VAL Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 12 ILE Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 6 residue 56 LEU Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 173 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 180 optimal weight: 0.0770 chunk 201 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 408 GLN 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 18404 Z= 0.336 Angle : 0.618 7.660 24955 Z= 0.311 Chirality : 0.042 0.171 2805 Planarity : 0.004 0.054 3164 Dihedral : 11.827 163.499 2760 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.60 % Allowed : 24.84 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2228 helix: 1.80 (0.19), residues: 807 sheet: -0.26 (0.24), residues: 506 loop : -0.72 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 2 158 HIS 0.005 0.001 HIS 5 27 PHE 0.010 0.001 PHE 2 230 TYR 0.017 0.001 TYR 1 943 ARG 0.007 0.000 ARG10 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 96 time to evaluate : 2.005 Fit side-chains revert: symmetry clash REVERT: 2 183 MET cc_start: 0.8842 (mtp) cc_final: 0.8507 (mtt) REVERT: 2 254 MET cc_start: 0.9270 (mtp) cc_final: 0.8758 (mmm) REVERT: 3 130 MET cc_start: 0.8616 (mmm) cc_final: 0.8276 (mmm) REVERT: 3 251 MET cc_start: 0.8703 (tpp) cc_final: 0.7877 (tmm) REVERT: 5 31 MET cc_start: 0.8371 (tpp) cc_final: 0.8100 (tpp) REVERT: 8 134 MET cc_start: 0.8370 (mmt) cc_final: 0.7256 (tpp) REVERT: 10 186 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7482 (tm-30) outliers start: 86 outliers final: 46 residues processed: 174 average time/residue: 0.2642 time to fit residues: 76.2738 Evaluate side-chains 137 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 91 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 452 VAL Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 978 ILE Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 34 VAL Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 56 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 215 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 192 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18404 Z= 0.294 Angle : 0.598 7.723 24955 Z= 0.301 Chirality : 0.042 0.152 2805 Planarity : 0.004 0.049 3164 Dihedral : 11.425 164.927 2759 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.07 % Allowed : 25.64 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2228 helix: 1.83 (0.18), residues: 811 sheet: -0.29 (0.24), residues: 508 loop : -0.67 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 187 HIS 0.006 0.001 HIS 1 93 PHE 0.023 0.001 PHE 2 230 TYR 0.017 0.001 TYR 3 78 ARG 0.003 0.000 ARG 6 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 95 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 726 MET cc_start: 0.7808 (tpp) cc_final: 0.7573 (tpp) REVERT: 2 183 MET cc_start: 0.8835 (mtp) cc_final: 0.8508 (mtt) REVERT: 2 254 MET cc_start: 0.9292 (mtp) cc_final: 0.8779 (mmm) REVERT: 3 130 MET cc_start: 0.8585 (mmm) cc_final: 0.8235 (mmm) REVERT: 3 251 MET cc_start: 0.8700 (tpp) cc_final: 0.7869 (tmm) REVERT: 5 31 MET cc_start: 0.8394 (tpp) cc_final: 0.8090 (tpp) REVERT: 5 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8701 (mpp) REVERT: 8 134 MET cc_start: 0.8351 (mmt) cc_final: 0.7234 (tpp) REVERT: 10 186 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7455 (tm-30) outliers start: 76 outliers final: 49 residues processed: 165 average time/residue: 0.2735 time to fit residues: 73.8010 Evaluate side-chains 139 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 90 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 452 VAL Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 978 ILE Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 31 THR Chi-restraints excluded: chain 6 residue 68 LEU Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 183 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 148 optimal weight: 40.0000 chunk 0 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18404 Z= 0.242 Angle : 0.581 7.937 24955 Z= 0.292 Chirality : 0.041 0.156 2805 Planarity : 0.003 0.050 3164 Dihedral : 11.002 166.681 2759 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.07 % Allowed : 25.70 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2228 helix: 1.88 (0.19), residues: 812 sheet: -0.25 (0.24), residues: 507 loop : -0.62 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 187 HIS 0.004 0.001 HIS 8 62 PHE 0.019 0.001 PHE 2 230 TYR 0.014 0.001 TYR 1 943 ARG 0.005 0.000 ARG10 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 93 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 293 LEU cc_start: 0.9761 (OUTLIER) cc_final: 0.9546 (tt) REVERT: 1 726 MET cc_start: 0.7876 (tpp) cc_final: 0.7624 (tpp) REVERT: 2 183 MET cc_start: 0.8843 (mtp) cc_final: 0.8529 (mtt) REVERT: 2 254 MET cc_start: 0.9298 (mtp) cc_final: 0.8757 (mmm) REVERT: 3 130 MET cc_start: 0.8500 (mmm) cc_final: 0.7942 (mmm) REVERT: 3 251 MET cc_start: 0.8673 (tpp) cc_final: 0.7882 (tmm) REVERT: 5 31 MET cc_start: 0.8379 (tpp) cc_final: 0.8095 (tpp) REVERT: 5 70 MET cc_start: 0.9067 (mtp) cc_final: 0.8626 (mpp) REVERT: 7 162 MET cc_start: 0.7953 (pmm) cc_final: 0.7700 (pmm) REVERT: 10 186 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7445 (tm-30) outliers start: 76 outliers final: 57 residues processed: 163 average time/residue: 0.2690 time to fit residues: 73.0904 Evaluate side-chains 149 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 91 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 293 LEU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 436 LEU Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 540 THR Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 725 VAL Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 844 ILE Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 978 ILE Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 68 LEU Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 187 LEU Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 26 GLN ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 : 0.004 0.056 18404 Z= 0.273 Angle : 0.594 11.409 24955 Z= 0.296 Chirality : 0.041 0.157 2805 Planarity : 0.004 0.051 3164 Dihedral : 10.712 168.251 2759 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.14 % Allowed : 25.64 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 2228 helix: 1.88 (0.19), residues: 818 sheet: -0.27 (0.24), residues: 506 loop : -0.62 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP 2 158 HIS 0.004 0.001 HIS 8 62 PHE 0.019 0.001 PHE 2 230 TYR 0.015 0.001 TYR 1 943 ARG 0.003 0.000 ARG10 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 94 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 293 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9554 (tt) REVERT: 1 726 MET cc_start: 0.7970 (tpp) cc_final: 0.7512 (tpp) REVERT: 2 183 MET cc_start: 0.8845 (mtp) cc_final: 0.8518 (mtt) REVERT: 2 254 MET cc_start: 0.9300 (mtp) cc_final: 0.8765 (mmm) REVERT: 3 130 MET cc_start: 0.8557 (mmm) cc_final: 0.8091 (mmm) REVERT: 3 251 MET cc_start: 0.8702 (tpp) cc_final: 0.7790 (tmm) REVERT: 5 31 MET cc_start: 0.8366 (tpp) cc_final: 0.8113 (tpp) REVERT: 8 134 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7333 (tpp) REVERT: 10 186 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7448 (tm-30) outliers start: 96 outliers final: 66 residues processed: 181 average time/residue: 0.2700 time to fit residues: 79.8494 Evaluate side-chains 158 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 90 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 293 LEU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 436 LEU Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 540 THR Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 725 VAL Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 784 ILE Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 844 ILE Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 965 ILE Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 978 ILE Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 34 VAL Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 4 residue 165 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 31 THR Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 131 optimal weight: 0.3980 chunk 99 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1865 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: