Starting phenix.real_space_refine on Sun Aug 24 08:23:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9s_40245/08_2025/8s9s_40245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9s_40245/08_2025/8s9s_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/cci-nas-00/data/ceres_data/8s9s_40245/08_2025/8s9s_40245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9s_40245/08_2025/8s9s_40245.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9s_40245/08_2025/8s9s_40245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9s_40245/08_2025/8s9s_40245.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 5, 'ASN:plan1': 3, 'PHE:plan': 4, 'TYR:plan': 3} 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: 4.19, per 1000 atoms: 0.23 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: 1.69 Conformation dependent library (CDL) restraints added in 778.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.71 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: 3.52 Time building geometry restraints manager: 2.20 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: 4.540 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.840 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- 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 18413 Z= 0.231 Angle : 0.826 25.267 24980 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG 7 119 TYR 0.021 0.001 TYR 1 912 PHE 0.016 0.001 PHE 2 230 TRP 0.055 0.002 TRP 2 158 HIS 0.003 0.001 HIS 2 187 Details of bonding type rmsd covalent geometry : bond 0.00493 (18404) covalent geometry : angle 0.82416 (24955) SS BOND : bond 0.00555 ( 2) SS BOND : angle 2.22133 ( 4) hydrogen bonds : bond 0.14717 ( 844) hydrogen bonds : angle 6.57104 ( 2409) link_BETA1-4 : bond 0.00203 ( 3) link_BETA1-4 : angle 1.90366 ( 9) link_NAG-ASN : bond 0.00149 ( 4) link_NAG-ASN : angle 2.12032 ( 12) *********************** 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 : 0.757 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: 0.8816 (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: 0.1321 time to fit residues: 25.9802 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 : 0.715 ------------------------------------------------------------------------------- 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 216 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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** 8 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.051289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.034480 restraints weight = 107861.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.035729 restraints weight = 49727.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036502 restraints weight = 32834.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.036947 restraints weight = 26124.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.037169 restraints weight = 23079.710| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 18413 Z= 0.248 Angle : 0.644 7.586 24980 Z= 0.328 Chirality : 0.042 0.158 2805 Planarity : 0.004 0.064 3164 Dihedral : 12.466 165.452 2771 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.28 % Allowed : 24.84 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.18), residues: 2228 helix: 1.71 (0.19), residues: 797 sheet: -0.39 (0.24), residues: 511 loop : -0.72 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 273 TYR 0.018 0.002 TYR 1 943 PHE 0.020 0.001 PHE 2 230 TRP 0.025 0.002 TRP 2 158 HIS 0.004 0.001 HIS 1 783 Details of bonding type rmsd covalent geometry : bond 0.00549 (18404) covalent geometry : angle 0.64172 (24955) SS BOND : bond 0.00325 ( 2) SS BOND : angle 1.53817 ( 4) hydrogen bonds : bond 0.04121 ( 844) hydrogen bonds : angle 5.18564 ( 2409) link_BETA1-4 : bond 0.00151 ( 3) link_BETA1-4 : angle 1.66173 ( 9) link_NAG-ASN : bond 0.00447 ( 4) link_NAG-ASN : angle 2.07658 ( 12) *********************** 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 174 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 94 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 408 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8817 (pt0) REVERT: 1 726 MET cc_start: 0.8524 (tpp) cc_final: 0.7871 (tpp) REVERT: 2 19 MET cc_start: 0.9495 (mmm) cc_final: 0.9025 (mmm) REVERT: 2 183 MET cc_start: 0.9161 (mtp) cc_final: 0.8810 (mtt) REVERT: 2 226 MET cc_start: 0.8008 (ppp) cc_final: 0.7635 (ppp) REVERT: 2 254 MET cc_start: 0.9403 (mtp) cc_final: 0.8985 (mmm) REVERT: 3 251 MET cc_start: 0.8980 (tpp) cc_final: 0.7891 (tmm) REVERT: 4 175 GLU cc_start: 0.8394 (mp0) cc_final: 0.8116 (mp0) REVERT: 8 71 LEU cc_start: 0.9765 (OUTLIER) cc_final: 0.9494 (pp) REVERT: 8 85 HIS cc_start: 0.9493 (OUTLIER) cc_final: 0.9269 (m90) outliers start: 80 outliers final: 43 residues processed: 164 average time/residue: 0.1230 time to fit residues: 33.6032 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 : 0.670 ------------------------------------------------------------------------------- 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 107 MET Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 191 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 408 GLN 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 757 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 93 THR Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 2 residue 280 TYR 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 6 residue 67 ILE Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 78 ILE Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 173 VAL Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 108 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 202 optimal weight: 0.0770 chunk 210 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- 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** 1 775 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.052037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.035209 restraints weight = 108636.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.036507 restraints weight = 49007.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.037317 restraints weight = 32046.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.037776 restraints weight = 25397.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.038035 restraints weight = 22429.417| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18413 Z= 0.131 Angle : 0.570 7.562 24980 Z= 0.288 Chirality : 0.041 0.169 2805 Planarity : 0.004 0.054 3164 Dihedral : 11.799 163.428 2760 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.80 % Allowed : 25.54 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.18), residues: 2228 helix: 1.80 (0.18), residues: 813 sheet: -0.30 (0.24), residues: 507 loop : -0.64 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG10 204 TYR 0.011 0.001 TYR 1 672 PHE 0.013 0.001 PHE 2 230 TRP 0.014 0.001 TRP 1 187 HIS 0.004 0.001 HIS 8 62 Details of bonding type rmsd covalent geometry : bond 0.00291 (18404) covalent geometry : angle 0.56757 (24955) SS BOND : bond 0.00208 ( 2) SS BOND : angle 1.29419 ( 4) hydrogen bonds : bond 0.03625 ( 844) hydrogen bonds : angle 4.83223 ( 2409) link_BETA1-4 : bond 0.00304 ( 3) link_BETA1-4 : angle 1.67638 ( 9) link_NAG-ASN : bond 0.00148 ( 4) link_NAG-ASN : angle 1.94093 ( 12) *********************** 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 167 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 96 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8937 (m-40) REVERT: 1 408 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8882 (pt0) REVERT: 1 640 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9233 (tp) REVERT: 1 726 MET cc_start: 0.8379 (tpp) cc_final: 0.7829 (tpp) REVERT: 2 183 MET cc_start: 0.9116 (mtp) cc_final: 0.8776 (mtt) REVERT: 2 254 MET cc_start: 0.9418 (mtp) cc_final: 0.8995 (mmm) REVERT: 3 130 MET cc_start: 0.8928 (mmm) cc_final: 0.8483 (mmm) REVERT: 3 251 MET cc_start: 0.8933 (tpp) cc_final: 0.7857 (tmm) REVERT: 5 70 MET cc_start: 0.9233 (mtp) cc_final: 0.8627 (mpp) REVERT: 7 118 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8234 (ppp) REVERT: 8 71 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9466 (pp) REVERT: 8 134 MET cc_start: 0.8592 (mmt) cc_final: 0.7364 (tpp) REVERT: 10 186 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7223 (tm-30) outliers start: 71 outliers final: 39 residues processed: 160 average time/residue: 0.0974 time to fit residues: 26.0303 Evaluate side-chains 134 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 90 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 93 HIS 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 408 GLN Chi-restraints excluded: chain 1 residue 422 LEU 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 603 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 640 LEU 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 963 VAL 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 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 68 LEU Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 118 MET Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 10 residue 85 LEU Chi-restraints excluded: chain 10 residue 112 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 chunk 120 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 219 optimal weight: 0.0270 chunk 118 optimal weight: 5.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- 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** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.052293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.035485 restraints weight = 108378.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.036806 restraints weight = 47943.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.037617 restraints weight = 31065.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.038106 restraints weight = 24551.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.038332 restraints weight = 21521.000| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18413 Z= 0.110 Angle : 0.562 7.476 24980 Z= 0.281 Chirality : 0.041 0.147 2805 Planarity : 0.003 0.050 3164 Dihedral : 11.328 164.461 2759 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.64 % Allowed : 25.43 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 2228 helix: 1.83 (0.18), residues: 811 sheet: -0.16 (0.24), residues: 506 loop : -0.59 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 273 TYR 0.016 0.001 TYR 3 78 PHE 0.024 0.001 PHE 2 230 TRP 0.012 0.001 TRP 1 187 HIS 0.005 0.001 HIS 1 93 Details of bonding type rmsd covalent geometry : bond 0.00246 (18404) covalent geometry : angle 0.55946 (24955) SS BOND : bond 0.00207 ( 2) SS BOND : angle 1.09838 ( 4) hydrogen bonds : bond 0.03371 ( 844) hydrogen bonds : angle 4.68680 ( 2409) link_BETA1-4 : bond 0.00355 ( 3) link_BETA1-4 : angle 1.67948 ( 9) link_NAG-ASN : bond 0.00128 ( 4) link_NAG-ASN : angle 1.93179 ( 12) *********************** 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 164 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 96 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8885 (m-40) REVERT: 1 408 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8885 (pt0) REVERT: 2 183 MET cc_start: 0.9113 (mtp) cc_final: 0.8798 (mtt) REVERT: 2 254 MET cc_start: 0.9463 (mtp) cc_final: 0.9027 (mmm) REVERT: 3 106 MET cc_start: 0.7400 (ptt) cc_final: 0.7195 (tmm) REVERT: 3 130 MET cc_start: 0.8937 (mmm) cc_final: 0.8449 (mmm) REVERT: 3 251 MET cc_start: 0.8923 (tpp) cc_final: 0.7807 (tmm) REVERT: 5 70 MET cc_start: 0.9222 (mtp) cc_final: 0.8579 (mpp) REVERT: 7 117 LYS cc_start: 0.8980 (tppt) cc_final: 0.8679 (tppt) REVERT: 7 118 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8177 (ppp) REVERT: 7 162 MET cc_start: 0.8024 (pmm) cc_final: 0.7765 (pmm) REVERT: 8 71 LEU cc_start: 0.9768 (OUTLIER) cc_final: 0.9470 (pp) REVERT: 10 186 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7135 (tm-30) outliers start: 68 outliers final: 41 residues processed: 157 average time/residue: 0.1017 time to fit residues: 26.9122 Evaluate side-chains 135 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 90 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN 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 229 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 408 GLN 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 603 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 912 TYR Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 963 VAL 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 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 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 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 118 MET Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 85 LEU Chi-restraints excluded: chain 10 residue 112 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 219 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.051891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.035081 restraints weight = 107626.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.036367 restraints weight = 48772.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.037163 restraints weight = 31933.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.037634 restraints weight = 25315.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.037849 restraints weight = 22311.061| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18413 Z= 0.145 Angle : 0.565 8.854 24980 Z= 0.283 Chirality : 0.041 0.161 2805 Planarity : 0.003 0.050 3164 Dihedral : 10.951 165.957 2759 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.85 % Allowed : 25.43 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2228 helix: 1.85 (0.18), residues: 818 sheet: -0.11 (0.24), residues: 502 loop : -0.58 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG10 204 TYR 0.012 0.001 TYR 3 78 PHE 0.021 0.001 PHE 2 230 TRP 0.011 0.001 TRP 1 187 HIS 0.003 0.001 HIS 1 93 Details of bonding type rmsd covalent geometry : bond 0.00326 (18404) covalent geometry : angle 0.56289 (24955) SS BOND : bond 0.00197 ( 2) SS BOND : angle 1.13440 ( 4) hydrogen bonds : bond 0.03341 ( 844) hydrogen bonds : angle 4.64245 ( 2409) link_BETA1-4 : bond 0.00219 ( 3) link_BETA1-4 : angle 1.69270 ( 9) link_NAG-ASN : bond 0.00153 ( 4) link_NAG-ASN : angle 2.01826 ( 12) *********************** 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 164 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 92 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8931 (m-40) REVERT: 1 109 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8098 (p) REVERT: 1 293 LEU cc_start: 0.9824 (OUTLIER) cc_final: 0.9580 (tp) REVERT: 1 408 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8940 (pt0) REVERT: 1 726 MET cc_start: 0.8292 (tpp) cc_final: 0.7969 (tpp) REVERT: 2 158 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.8464 (m-10) REVERT: 2 183 MET cc_start: 0.9081 (mtp) cc_final: 0.8759 (mtt) REVERT: 2 254 MET cc_start: 0.9461 (mtp) cc_final: 0.9025 (mmm) REVERT: 3 130 MET cc_start: 0.8907 (mmm) cc_final: 0.8250 (mmm) REVERT: 3 251 MET cc_start: 0.8864 (tpp) cc_final: 0.7830 (tmm) REVERT: 5 31 MET cc_start: 0.8471 (tpp) cc_final: 0.8235 (tpp) REVERT: 5 70 MET cc_start: 0.9204 (mtp) cc_final: 0.8576 (mpp) REVERT: 7 118 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8263 (ppp) REVERT: 8 71 LEU cc_start: 0.9757 (OUTLIER) cc_final: 0.9450 (pp) REVERT: 8 134 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7361 (tpp) REVERT: 10 186 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7189 (tm-30) REVERT: 10 204 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8852 (mtm110) outliers start: 72 outliers final: 52 residues processed: 156 average time/residue: 0.1003 time to fit residues: 26.1737 Evaluate side-chains 150 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 89 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 109 SER 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 408 GLN Chi-restraints excluded: chain 1 residue 436 LEU 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 603 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 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 966 SER Chi-restraints excluded: chain 1 residue 976 THR 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 158 TRP 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 7 residue 118 MET Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 187 LEU Chi-restraints excluded: chain 10 residue 204 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 151 optimal weight: 30.0000 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 203 optimal weight: 30.0000 chunk 56 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 238 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.051633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.034769 restraints weight = 107399.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.036044 restraints weight = 48921.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.036830 restraints weight = 32179.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.037266 restraints weight = 25644.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.037553 restraints weight = 22717.294| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18413 Z= 0.161 Angle : 0.572 10.917 24980 Z= 0.286 Chirality : 0.041 0.156 2805 Planarity : 0.003 0.052 3164 Dihedral : 10.650 167.175 2759 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.44 % Allowed : 25.64 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.19), residues: 2228 helix: 1.90 (0.19), residues: 818 sheet: -0.08 (0.24), residues: 496 loop : -0.57 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 6 73 TYR 0.018 0.001 TYR 3 78 PHE 0.021 0.001 PHE 2 230 TRP 0.012 0.001 TRP 1 187 HIS 0.003 0.001 HIS 8 62 Details of bonding type rmsd covalent geometry : bond 0.00360 (18404) covalent geometry : angle 0.56928 (24955) SS BOND : bond 0.00214 ( 2) SS BOND : angle 1.17927 ( 4) hydrogen bonds : bond 0.03319 ( 844) hydrogen bonds : angle 4.62450 ( 2409) link_BETA1-4 : bond 0.00229 ( 3) link_BETA1-4 : angle 1.79145 ( 9) link_NAG-ASN : bond 0.00175 ( 4) link_NAG-ASN : angle 2.06709 ( 12) *********************** 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 177 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 94 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8923 (m-40) REVERT: 1 109 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8122 (p) REVERT: 1 293 LEU cc_start: 0.9831 (OUTLIER) cc_final: 0.9616 (tt) REVERT: 1 408 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8982 (pt0) REVERT: 1 726 MET cc_start: 0.8347 (tpp) cc_final: 0.8045 (tpp) REVERT: 2 183 MET cc_start: 0.9089 (mtp) cc_final: 0.8772 (mtt) REVERT: 2 254 MET cc_start: 0.9462 (mtp) cc_final: 0.8888 (mmm) REVERT: 3 130 MET cc_start: 0.8898 (mmm) cc_final: 0.8292 (mmm) REVERT: 3 251 MET cc_start: 0.8870 (tpp) cc_final: 0.7875 (tmm) REVERT: 5 31 MET cc_start: 0.8503 (tpp) cc_final: 0.8253 (tpp) REVERT: 5 70 MET cc_start: 0.9202 (mtp) cc_final: 0.8551 (mpp) REVERT: 7 118 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8259 (ppp) REVERT: 7 122 TYR cc_start: 0.8122 (t80) cc_final: 0.7894 (t80) REVERT: 7 162 MET cc_start: 0.7935 (pmm) cc_final: 0.7644 (pmm) REVERT: 8 71 LEU cc_start: 0.9763 (OUTLIER) cc_final: 0.9470 (pp) REVERT: 8 134 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7258 (tpp) REVERT: 10 186 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7232 (tm-30) outliers start: 83 outliers final: 55 residues processed: 170 average time/residue: 0.1079 time to fit residues: 30.3811 Evaluate side-chains 150 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 88 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 61 ASN 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 109 SER 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 408 GLN Chi-restraints excluded: chain 1 residue 436 LEU 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 603 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 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 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 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 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 97 VAL Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 118 MET Chi-restraints excluded: chain 8 residue 71 LEU 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 138 VAL 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 99 optimal weight: 0.9980 chunk 219 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.052086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.035352 restraints weight = 107907.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.036663 restraints weight = 47694.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.037481 restraints weight = 30858.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.037954 restraints weight = 24336.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.038174 restraints weight = 21398.785| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 18413 Z= 0.110 Angle : 0.572 10.082 24980 Z= 0.284 Chirality : 0.041 0.155 2805 Planarity : 0.003 0.053 3164 Dihedral : 10.416 167.906 2759 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.43 % Allowed : 26.45 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.19), residues: 2228 helix: 1.87 (0.19), residues: 818 sheet: -0.08 (0.24), residues: 504 loop : -0.52 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG10 204 TYR 0.019 0.001 TYR 8 87 PHE 0.021 0.001 PHE 2 230 TRP 0.012 0.001 TRP 1 187 HIS 0.007 0.001 HIS 8 85 Details of bonding type rmsd covalent geometry : bond 0.00247 (18404) covalent geometry : angle 0.56992 (24955) SS BOND : bond 0.00199 ( 2) SS BOND : angle 1.08904 ( 4) hydrogen bonds : bond 0.03242 ( 844) hydrogen bonds : angle 4.53070 ( 2409) link_BETA1-4 : bond 0.00338 ( 3) link_BETA1-4 : angle 1.75051 ( 9) link_NAG-ASN : bond 0.00093 ( 4) link_NAG-ASN : angle 1.98037 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 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 155 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 91 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8883 (m-40) REVERT: 1 109 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8089 (p) REVERT: 1 293 LEU cc_start: 0.9825 (OUTLIER) cc_final: 0.9571 (tp) REVERT: 1 726 MET cc_start: 0.8314 (tpp) cc_final: 0.8032 (tpp) REVERT: 2 183 MET cc_start: 0.9051 (mtp) cc_final: 0.8735 (mtt) REVERT: 2 254 MET cc_start: 0.9455 (mtp) cc_final: 0.8871 (mmm) REVERT: 3 130 MET cc_start: 0.8923 (mmm) cc_final: 0.8252 (mmm) REVERT: 3 251 MET cc_start: 0.8847 (tpp) cc_final: 0.7853 (tmm) REVERT: 5 31 MET cc_start: 0.8487 (tpp) cc_final: 0.8238 (tpp) REVERT: 5 70 MET cc_start: 0.9207 (mtp) cc_final: 0.8553 (mpp) REVERT: 7 118 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8306 (ppp) REVERT: 7 122 TYR cc_start: 0.8110 (t80) cc_final: 0.7901 (t80) REVERT: 8 71 LEU cc_start: 0.9754 (OUTLIER) cc_final: 0.9461 (pp) REVERT: 8 134 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7375 (tpp) REVERT: 10 186 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7255 (tm-30) outliers start: 64 outliers final: 48 residues processed: 148 average time/residue: 0.1145 time to fit residues: 28.6987 Evaluate side-chains 143 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 89 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 45 LEU Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 61 ASN 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 109 SER 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 436 LEU 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 603 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 912 TYR Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 972 LEU Chi-restraints excluded: chain 1 residue 982 LEU 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 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 6 residue 15 SER 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 7 residue 118 MET Chi-restraints excluded: chain 8 residue 71 LEU 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 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 2 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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** 1 408 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.052056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.034337 restraints weight = 109070.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.035606 restraints weight = 50408.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.036390 restraints weight = 33266.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.036853 restraints weight = 26546.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.037068 restraints weight = 23440.780| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 18413 Z= 0.238 Angle : 0.630 10.267 24980 Z= 0.314 Chirality : 0.042 0.188 2805 Planarity : 0.004 0.054 3164 Dihedral : 10.362 169.999 2759 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.01 % Allowed : 26.12 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.19), residues: 2228 helix: 1.90 (0.19), residues: 822 sheet: -0.19 (0.24), residues: 500 loop : -0.61 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG10 204 TYR 0.017 0.001 TYR 7 136 PHE 0.020 0.001 PHE 2 230 TRP 0.062 0.002 TRP 2 158 HIS 0.004 0.001 HIS 5 27 Details of bonding type rmsd covalent geometry : bond 0.00526 (18404) covalent geometry : angle 0.62756 (24955) SS BOND : bond 0.00236 ( 2) SS BOND : angle 1.32387 ( 4) hydrogen bonds : bond 0.03446 ( 844) hydrogen bonds : angle 4.68820 ( 2409) link_BETA1-4 : bond 0.00228 ( 3) link_BETA1-4 : angle 1.88116 ( 9) link_NAG-ASN : bond 0.00382 ( 4) link_NAG-ASN : angle 2.24057 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 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 167 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 92 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8924 (m-40) REVERT: 1 293 LEU cc_start: 0.9848 (OUTLIER) cc_final: 0.9633 (tt) REVERT: 1 726 MET cc_start: 0.8561 (tpp) cc_final: 0.8305 (tpp) REVERT: 2 183 MET cc_start: 0.9121 (mtp) cc_final: 0.8811 (mtt) REVERT: 2 254 MET cc_start: 0.9474 (mtp) cc_final: 0.8900 (mmm) REVERT: 3 130 MET cc_start: 0.8928 (mmm) cc_final: 0.8265 (mmm) REVERT: 3 251 MET cc_start: 0.8922 (tpp) cc_final: 0.7801 (tmm) REVERT: 5 31 MET cc_start: 0.8480 (tpp) cc_final: 0.8255 (tpp) REVERT: 7 118 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8238 (ppp) REVERT: 7 122 TYR cc_start: 0.8182 (t80) cc_final: 0.7936 (t80) REVERT: 8 71 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9467 (pp) REVERT: 8 134 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7244 (tpp) REVERT: 10 186 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7266 (tm-30) outliers start: 75 outliers final: 56 residues processed: 158 average time/residue: 0.1215 time to fit residues: 31.5776 Evaluate side-chains 151 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 90 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 45 LEU Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 61 ASN 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 331 THR Chi-restraints excluded: chain 1 residue 436 LEU 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 603 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 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 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 966 SER Chi-restraints excluded: chain 1 residue 972 LEU 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 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 84 LEU Chi-restraints excluded: chain 6 residue 15 SER 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 118 MET Chi-restraints excluded: chain 8 residue 71 LEU 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 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 44 optimal weight: 7.9990 chunk 150 optimal weight: 0.0050 chunk 106 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 170 optimal weight: 0.0270 chunk 27 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.0058 ------------------------------------------------------------------------------- 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** ** 1 794 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.051356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.034572 restraints weight = 107650.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.035835 restraints weight = 48780.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.036618 restraints weight = 32020.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.037078 restraints weight = 25465.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.037290 restraints weight = 22482.422| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18413 Z= 0.150 Angle : 0.591 9.574 24980 Z= 0.293 Chirality : 0.041 0.163 2805 Planarity : 0.003 0.057 3164 Dihedral : 10.190 171.008 2759 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.48 % Allowed : 26.39 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.19), residues: 2228 helix: 1.93 (0.19), residues: 820 sheet: -0.13 (0.24), residues: 496 loop : -0.58 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG10 204 TYR 0.015 0.001 TYR 7 136 PHE 0.019 0.001 PHE 2 230 TRP 0.050 0.001 TRP 2 158 HIS 0.004 0.001 HIS 8 62 Details of bonding type rmsd covalent geometry : bond 0.00340 (18404) covalent geometry : angle 0.58857 (24955) SS BOND : bond 0.00215 ( 2) SS BOND : angle 1.25537 ( 4) hydrogen bonds : bond 0.03305 ( 844) hydrogen bonds : angle 4.57842 ( 2409) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 1.89532 ( 9) link_NAG-ASN : bond 0.00140 ( 4) link_NAG-ASN : angle 2.09024 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 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 156 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 91 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8895 (m-40) REVERT: 1 293 LEU cc_start: 0.9845 (OUTLIER) cc_final: 0.9630 (tt) REVERT: 1 726 MET cc_start: 0.8475 (tpp) cc_final: 0.7849 (tpp) REVERT: 2 183 MET cc_start: 0.9119 (mtp) cc_final: 0.8813 (mtt) REVERT: 2 254 MET cc_start: 0.9461 (mtp) cc_final: 0.8857 (mmm) REVERT: 3 130 MET cc_start: 0.8911 (mmm) cc_final: 0.8589 (mmm) REVERT: 3 242 MET cc_start: 0.9184 (mmp) cc_final: 0.8898 (mmp) REVERT: 3 251 MET cc_start: 0.8890 (tpp) cc_final: 0.7779 (tmm) REVERT: 5 31 MET cc_start: 0.8480 (tpp) cc_final: 0.8191 (tpp) REVERT: 5 70 MET cc_start: 0.9286 (mtp) cc_final: 0.8629 (mpp) REVERT: 7 118 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8074 (ppp) REVERT: 7 122 TYR cc_start: 0.8154 (t80) cc_final: 0.7934 (t80) REVERT: 8 71 LEU cc_start: 0.9771 (OUTLIER) cc_final: 0.9472 (pp) REVERT: 8 134 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7244 (tpp) REVERT: 10 142 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9298 (tt) REVERT: 10 186 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7202 (tm-30) outliers start: 65 outliers final: 56 residues processed: 147 average time/residue: 0.1173 time to fit residues: 29.0299 Evaluate side-chains 152 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 90 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 45 LEU Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN 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 436 LEU 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 603 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 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 972 LEU Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 982 LEU 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 6 residue 15 SER Chi-restraints excluded: chain 6 residue 36 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 118 MET Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain 8 residue 71 LEU 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 138 VAL Chi-restraints excluded: chain 10 residue 142 LEU Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 52 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 221 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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** ** 1 794 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.051596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.034820 restraints weight = 107965.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036094 restraints weight = 48791.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.036886 restraints weight = 31974.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.037340 restraints weight = 25414.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.037602 restraints weight = 22470.050| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18413 Z= 0.133 Angle : 0.588 9.457 24980 Z= 0.291 Chirality : 0.041 0.170 2805 Planarity : 0.003 0.058 3164 Dihedral : 9.985 172.452 2759 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.37 % Allowed : 26.55 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.19), residues: 2228 helix: 1.91 (0.19), residues: 822 sheet: -0.12 (0.24), residues: 496 loop : -0.53 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG10 204 TYR 0.014 0.001 TYR 7 136 PHE 0.020 0.001 PHE 2 230 TRP 0.057 0.001 TRP 2 158 HIS 0.004 0.001 HIS 8 62 Details of bonding type rmsd covalent geometry : bond 0.00303 (18404) covalent geometry : angle 0.58476 (24955) SS BOND : bond 0.00214 ( 2) SS BOND : angle 1.19961 ( 4) hydrogen bonds : bond 0.03234 ( 844) hydrogen bonds : angle 4.51443 ( 2409) link_BETA1-4 : bond 0.00295 ( 3) link_BETA1-4 : angle 1.90817 ( 9) link_NAG-ASN : bond 0.00100 ( 4) link_NAG-ASN : angle 2.06623 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 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 158 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 95 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8882 (m-40) REVERT: 1 293 LEU cc_start: 0.9842 (OUTLIER) cc_final: 0.9627 (tt) REVERT: 1 726 MET cc_start: 0.8459 (tpp) cc_final: 0.7823 (tpp) REVERT: 2 183 MET cc_start: 0.9110 (mtp) cc_final: 0.8808 (mtt) REVERT: 2 254 MET cc_start: 0.9461 (mtp) cc_final: 0.8869 (mmm) REVERT: 3 130 MET cc_start: 0.8908 (mmm) cc_final: 0.8571 (mmm) REVERT: 3 251 MET cc_start: 0.8874 (tpp) cc_final: 0.7788 (tmm) REVERT: 5 31 MET cc_start: 0.8510 (tpp) cc_final: 0.8233 (tpp) REVERT: 5 70 MET cc_start: 0.9271 (mtp) cc_final: 0.8563 (mpp) REVERT: 7 118 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8082 (ppp) REVERT: 7 122 TYR cc_start: 0.8129 (t80) cc_final: 0.7922 (t80) REVERT: 8 71 LEU cc_start: 0.9770 (OUTLIER) cc_final: 0.9465 (pp) REVERT: 8 134 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.7210 (tpp) REVERT: 10 186 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7240 (tm-30) outliers start: 63 outliers final: 55 residues processed: 150 average time/residue: 0.1169 time to fit residues: 29.5192 Evaluate side-chains 152 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 92 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 45 LEU Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN 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 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 603 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 912 TYR Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 972 LEU Chi-restraints excluded: chain 1 residue 982 LEU 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 6 residue 15 SER Chi-restraints excluded: chain 6 residue 36 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 118 MET Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain 8 residue 71 LEU 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 138 VAL Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 191 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 190 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 63 optimal weight: 0.0030 chunk 24 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 overall best weight: 4.1196 ------------------------------------------------------------------------------- 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** ** 1 794 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** 8 149 ASN ** 8 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.050658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.033809 restraints weight = 108591.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.035046 restraints weight = 49677.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.035811 restraints weight = 32813.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036247 restraints weight = 26173.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.036504 restraints weight = 23227.321| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 18413 Z= 0.246 Angle : 0.643 9.607 24980 Z= 0.320 Chirality : 0.042 0.174 2805 Planarity : 0.004 0.056 3164 Dihedral : 10.027 174.569 2759 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.80 % Allowed : 26.02 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 2228 helix: 1.91 (0.19), residues: 817 sheet: -0.28 (0.24), residues: 499 loop : -0.62 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 8 150 TYR 0.021 0.002 TYR 7 136 PHE 0.018 0.001 PHE 2 230 TRP 0.055 0.002 TRP 2 158 HIS 0.004 0.001 HIS 5 27 Details of bonding type rmsd covalent geometry : bond 0.00545 (18404) covalent geometry : angle 0.63948 (24955) SS BOND : bond 0.00248 ( 2) SS BOND : angle 1.39726 ( 4) hydrogen bonds : bond 0.03445 ( 844) hydrogen bonds : angle 4.68784 ( 2409) link_BETA1-4 : bond 0.00060 ( 3) link_BETA1-4 : angle 2.06865 ( 9) link_NAG-ASN : bond 0.00392 ( 4) link_NAG-ASN : angle 2.28482 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3554.76 seconds wall clock time: 62 minutes 20.95 seconds (3740.95 seconds total)