Starting phenix.real_space_refine on Sun Mar 17 14:21:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/03_2024/8s9s_40245_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/03_2024/8s9s_40245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/03_2024/8s9s_40245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/03_2024/8s9s_40245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/03_2024/8s9s_40245_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9s_40245/03_2024/8s9s_40245_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 72 5.16 5 C 11530 2.51 5 N 3066 2.21 5 O 3338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 138": "OE1" <-> "OE2" Residue "1 GLU 169": "OE1" <-> "OE2" Residue "1 TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 206": "OD1" <-> "OD2" Residue "1 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 426": "OE1" <-> "OE2" Residue "1 GLU 447": "OE1" <-> "OE2" Residue "1 TYR 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 853": "OE1" <-> "OE2" Residue "2 PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 287": "OD1" <-> "OD2" Residue "2 GLU 290": "OE1" <-> "OE2" Residue "3 ASP 245": "OD1" <-> "OD2" Residue "4 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 49": "OD1" <-> "OD2" Residue "4 PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 44": "OD1" <-> "OD2" Residue "5 PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 70": "OD1" <-> "OD2" Residue "7 ASP 88": "OD1" <-> "OD2" Residue "7 ASP 111": "OD1" <-> "OD2" Residue "7 TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 153": "OE1" <-> "OE2" Residue "8 TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 191": "OD1" <-> "OD2" Residue "10 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18012 Number of models: 1 Model: "" Number of chains: 15 Chain: "1" Number of atoms: 7367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7367 Classifications: {'peptide': 930} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 886} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "2" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2306 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 276} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1833 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "4" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 867 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 10, 'TRANS': 133} Chain breaks: 2 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "5" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 795 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 97} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "6" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 774 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "7" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1054 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 124} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "8" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1533 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 8, 'TRANS': 183} Chain breaks: 1 Chain: "10" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1177 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 145} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "3" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 8 Chain: "6" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 9.90, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 8.97 Conformation dependent library (CDL) restraints added in 4.1 seconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 25 sheets defined 35.9% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain '1' and resid 83 through 85 No H-bonds generated for 'chain '1' and resid 83 through 85' Processing helix chain '1' and resid 262 through 264 No H-bonds generated for 'chain '1' and resid 262 through 264' Processing helix chain '1' and resid 447 through 450 Processing helix chain '1' and resid 464 through 470 removed outlier: 4.555A pdb=" N GLU 1 468 " --> pdb=" O GLY 1 464 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU 1 469 " --> pdb=" O ALA 1 465 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU 1 470 " --> pdb=" O GLN 1 466 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 464 through 470' Processing helix chain '1' and resid 480 through 501 removed outlier: 3.818A pdb=" N HIS 1 501 " --> pdb=" O ALA 1 497 " (cutoff:3.500A) Processing helix chain '1' and resid 656 through 664 Processing helix chain '1' and resid 666 through 668 No H-bonds generated for 'chain '1' and resid 666 through 668' Processing helix chain '1' and resid 875 through 878 Processing helix chain '1' and resid 888 through 893 Processing helix chain '1' and resid 906 through 908 No H-bonds generated for 'chain '1' and resid 906 through 908' Processing helix chain '1' and resid 962 through 992 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 12 through 24 Processing helix chain '2' and resid 30 through 43 Processing helix chain '2' and resid 50 through 66 removed outlier: 4.104A pdb=" N ILE 2 54 " --> pdb=" O ASP 2 51 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL 2 59 " --> pdb=" O TYR 2 56 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA 2 62 " --> pdb=" O VAL 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 82 removed outlier: 4.039A pdb=" N PHE 2 74 " --> pdb=" O ASP 2 70 " (cutoff:3.500A) Processing helix chain '2' and resid 87 through 100 removed outlier: 4.173A pdb=" N MET 2 100 " --> pdb=" O ARG 2 96 " (cutoff:3.500A) Processing helix chain '2' and resid 103 through 116 Processing helix chain '2' and resid 122 through 133 Processing helix chain '2' and resid 137 through 150 removed outlier: 3.900A pdb=" N GLN 2 150 " --> pdb=" O GLU 2 146 " (cutoff:3.500A) Processing helix chain '2' and resid 155 through 168 Processing helix chain '2' and resid 171 through 184 Processing helix chain '2' and resid 189 through 202 Processing helix chain '2' and resid 205 through 221 removed outlier: 4.554A pdb=" N LEU 2 210 " --> pdb=" O GLU 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 226 through 241 Processing helix chain '2' and resid 247 through 274 Processing helix chain '2' and resid 280 through 289 Processing helix chain '3' and resid 10 through 16 removed outlier: 3.630A pdb=" N LEU 3 14 " --> pdb=" O ASN 3 11 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP 3 15 " --> pdb=" O ILE 3 12 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL 3 16 " --> pdb=" O ARG 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 38 Processing helix chain '3' and resid 46 through 67 removed outlier: 6.232A pdb=" N LYS 3 66 " --> pdb=" O ARG 3 62 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYR 3 67 " --> pdb=" O GLU 3 63 " (cutoff:3.500A) Processing helix chain '3' and resid 70 through 80 Processing helix chain '3' and resid 105 through 117 removed outlier: 4.011A pdb=" N ASN 3 117 " --> pdb=" O GLY 3 113 " (cutoff:3.500A) Processing helix chain '3' and resid 119 through 131 Processing helix chain '3' and resid 146 through 152 Proline residue: 3 150 - end of helix Processing helix chain '3' and resid 168 through 177 Processing helix chain '3' and resid 180 through 186 Processing helix chain '3' and resid 215 through 227 Processing helix chain '3' and resid 233 through 235 No H-bonds generated for 'chain '3' and resid 233 through 235' Processing helix chain '3' and resid 237 through 242 Processing helix chain '4' and resid 68 through 90 Proline residue: 4 76 - end of helix Proline residue: 4 81 - end of helix Processing helix chain '4' and resid 92 through 95 No H-bonds generated for 'chain '4' and resid 92 through 95' Processing helix chain '4' and resid 98 through 107 removed outlier: 3.875A pdb=" N VAL 4 102 " --> pdb=" O PRO 4 98 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 114 No H-bonds generated for 'chain '4' and resid 111 through 114' Processing helix chain '4' and resid 116 through 122 Processing helix chain '4' and resid 127 through 154 Processing helix chain '4' and resid 162 through 167 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 34 Processing helix chain '5' and resid 43 through 63 removed outlier: 3.547A pdb=" N HIS 5 62 " --> pdb=" O TYR 5 58 " (cutoff:3.500A) Processing helix chain '5' and resid 81 through 84 No H-bonds generated for 'chain '5' and resid 81 through 84' Processing helix chain '5' and resid 88 through 90 No H-bonds generated for 'chain '5' and resid 88 through 90' Processing helix chain '5' and resid 96 through 100 Processing helix chain '6' and resid 16 through 44 Processing helix chain '6' and resid 48 through 70 removed outlier: 3.833A pdb=" N ILE 6 53 " --> pdb=" O TYR 6 50 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA 6 70 " --> pdb=" O ILE 6 67 " (cutoff:3.500A) Processing helix chain '6' and resid 74 through 76 No H-bonds generated for 'chain '6' and resid 74 through 76' Processing helix chain '6' and resid 81 through 86 removed outlier: 4.252A pdb=" N THR 6 86 " --> pdb=" O PRO 6 83 " (cutoff:3.500A) Processing helix chain '6' and resid 89 through 107 removed outlier: 3.586A pdb=" N THR 6 95 " --> pdb=" O GLY 6 91 " (cutoff:3.500A) Processing helix chain '7' and resid 58 through 64 removed outlier: 5.398A pdb=" N SER 7 63 " --> pdb=" O GLN 7 59 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA 7 64 " --> pdb=" O ASP 7 60 " (cutoff:3.500A) Processing helix chain '7' and resid 157 through 161 Processing helix chain '7' and resid 164 through 177 Proline residue: 7 172 - end of helix Processing helix chain '8' and resid 8 through 20 Processing helix chain '8' and resid 68 through 84 Processing helix chain '8' and resid 106 through 118 removed outlier: 4.267A pdb=" N GLY 8 118 " --> pdb=" O ARG 8 114 " (cutoff:3.500A) Processing helix chain '8' and resid 129 through 131 No H-bonds generated for 'chain '8' and resid 129 through 131' Processing helix chain '8' and resid 164 through 176 Processing helix chain '8' and resid 186 through 191 Processing helix chain '8' and resid 200 through 209 Processing helix chain '10' and resid 92 through 103 Processing helix chain '10' and resid 134 through 138 Processing helix chain '10' and resid 175 through 179 removed outlier: 3.626A pdb=" N GLU10 179 " --> pdb=" O VAL10 176 " (cutoff:3.500A) Processing helix chain '10' and resid 199 through 209 Processing sheet with id= A, first strand: chain '1' and resid 32 through 34 Processing sheet with id= B, first strand: chain '1' and resid 42 through 44 Processing sheet with id= C, 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: 3.643A pdb=" N TRP 1 119 " --> pdb=" O SER 1 109 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU 1 111 " --> pdb=" O LEU 1 117 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU 1 117 " --> pdb=" O GLU 1 111 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 128 through 134 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: 3.596A pdb=" N TRP 1 163 " --> pdb=" O LEU 1 153 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS 1 155 " --> pdb=" O LEU 1 161 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU 1 161 " --> pdb=" O HIS 1 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 174 through 181 removed outlier: 7.106A pdb=" N LEU 1 189 " --> pdb=" O GLN 1 176 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL 1 178 " --> pdb=" O TRP 1 187 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP 1 187 " --> pdb=" O VAL 1 178 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER 1 180 " --> pdb=" O VAL 1 185 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL 1 185 " --> pdb=" O SER 1 180 " (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= F, first strand: chain '1' and resid 228 through 230 Processing sheet with id= G, first strand: chain '1' and resid 275 through 277 removed outlier: 3.706A pdb=" N LYS 1 314 " --> pdb=" O LEU 1 302 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN 1 304 " --> pdb=" O LEU 1 312 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU 1 312 " --> pdb=" O GLN 1 304 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS 1 306 " --> pdb=" O LEU 1 310 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU 1 310 " --> pdb=" O HIS 1 306 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '1' and resid 322 through 326 Processing sheet with id= I, first strand: chain '1' and resid 430 through 433 Processing sheet with id= J, first strand: chain '1' and resid 452 through 458 removed outlier: 6.964A pdb=" N VAL 1 539 " --> pdb=" O VAL 1 453 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU 1 455 " --> pdb=" O VAL 1 537 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL 1 537 " --> pdb=" O LEU 1 455 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N MET 1 457 " --> pdb=" O MET 1 535 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET 1 535 " --> pdb=" O MET 1 457 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP 1 557 " --> pdb=" O GLY 1 547 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU 1 549 " --> pdb=" O ILE 1 555 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE 1 555 " --> pdb=" O GLU 1 549 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '1' and resid 599 through 604 removed outlier: 6.736A pdb=" N THR 1 588 " --> pdb=" O VAL 1 574 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL 1 574 " --> pdb=" O THR 1 588 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU 1 590 " --> pdb=" O LEU 1 572 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU 1 572 " --> pdb=" O LEU 1 590 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '1' and resid 649 through 652 removed outlier: 3.719A pdb=" N GLN 1 625 " --> pdb=" O ILE 1 643 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '1' and resid 671 through 675 Processing sheet with id= N, first strand: chain '1' and resid 723 through 725 Processing sheet with id= O, first strand: chain '1' and resid 772 through 776 removed outlier: 5.569A pdb=" N PHE 1 756 " --> pdb=" O SER 1 747 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU 1 746 " --> pdb=" O ILE 1 707 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE 1 707 " --> pdb=" O GLU 1 746 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '1' and resid 783 through 786 Processing sheet with id= Q, first strand: chain '1' and resid 795 through 797 Processing sheet with id= R, first strand: chain '1' and resid 807 through 811 Processing sheet with id= S, first strand: chain '1' and resid 860 through 864 Processing sheet with id= T, first strand: chain '7' and resid 47 through 49 Processing sheet with id= U, first strand: chain '7' and resid 74 through 77 Processing sheet with id= V, first strand: chain '8' and resid 4 through 6 removed outlier: 5.593A pdb=" N THR 8 52 " --> pdb=" O LYS 8 5 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain '8' and resid 150 through 153 removed outlier: 4.074A pdb=" N ALA 8 123 " --> pdb=" O ALA 8 90 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR 8 92 " --> pdb=" O ALA 8 123 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU 8 30 " --> pdb=" O ALA 8 90 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR 8 92 " --> pdb=" O GLY 8 28 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY 8 28 " --> pdb=" O TYR 8 92 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLN 8 94 " --> pdb=" O VAL 8 26 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL 8 26 " --> pdb=" O GLN 8 94 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN 8 27 " --> pdb=" O PHE 8 61 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE 8 61 " --> pdb=" O ASN 8 27 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU 8 29 " --> pdb=" O PRO 8 59 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL 8 31 " --> pdb=" O CYS 8 57 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS 8 57 " --> pdb=" O VAL 8 31 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '10' and resid 127 through 133 removed outlier: 6.225A pdb=" N LEU10 55 " --> pdb=" O PRO10 113 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS10 58 " --> pdb=" O LYS10 70 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS10 70 " --> pdb=" O HIS10 58 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER10 84 " --> pdb=" O LEU10 75 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '10' and resid 182 through 188 removed outlier: 3.515A pdb=" N VAL10 150 " --> pdb=" O GLN10 188 " (cutoff:3.500A) 753 hydrogen bonds defined for protein. 1896 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: 7.47 Time building geometry restraints manager: 9.28 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: 97.47 - 108.60: 1006 108.60 - 119.72: 15019 119.72 - 130.84: 8828 130.84 - 141.96: 101 141.96 - 153.09: 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: 1016 2.73 - 3.27: 18597 3.27 - 3.81: 30562 3.81 - 4.36: 34767 4.36 - 4.90: 59734 Nonbonded interactions: 144676 Sorted by model distance: nonbonded pdb=" OG SER10 140 " pdb=" OG SER10 143 " model vdw 2.184 2.440 nonbonded pdb=" O ALA 5 52 " pdb=" OG1 THR 5 56 " model vdw 2.195 2.440 nonbonded pdb=" O THR 3 137 " pdb=" OH TYR 6 110 " model vdw 2.198 2.440 nonbonded pdb=" OD1 ASP 5 82 " pdb=" NE2 HIS 8 62 " model vdw 2.205 2.520 nonbonded pdb=" OE2 GLU10 61 " pdb=" ND2 ASN10 67 " model vdw 2.221 2.520 ... (remaining 144671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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: 11.900 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: 0.000 Extract box with map and model: 10.710 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 55.790 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 18404 Z= 0.320 Angle : 0.824 25.267 24955 Z= 0.383 Chirality : 0.043 0.250 2805 Planarity : 0.005 0.131 3164 Dihedral : 18.618 175.582 6855 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.59 % Allowed : 28.32 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2228 helix: 1.19 (0.19), residues: 784 sheet: -0.32 (0.24), residues: 492 loop : -0.71 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP 2 158 HIS 0.003 0.001 HIS 2 187 PHE 0.016 0.001 PHE 2 230 TYR 0.021 0.001 TYR 1 912 ARG 0.008 0.000 ARG 7 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 726 MET cc_start: 0.7853 (tpp) cc_final: 0.7587 (tpp) REVERT: 2 19 MET cc_start: 0.9416 (mmm) cc_final: 0.9194 (mmm) REVERT: 2 183 MET cc_start: 0.8860 (mtp) cc_final: 0.8467 (mtt) REVERT: 2 254 MET cc_start: 0.9200 (mtp) cc_final: 0.8815 (mmm) REVERT: 3 251 MET cc_start: 0.8701 (tpp) cc_final: 0.7833 (tmm) outliers start: 11 outliers final: 6 residues processed: 121 average time/residue: 0.2669 time to fit residues: 51.6266 Evaluate side-chains 98 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 2 residue 230 PHE Chi-restraints excluded: chain 8 residue 195 ASN Chi-restraints excluded: chain 8 residue 204 LYS Chi-restraints excluded: chain 10 residue 173 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 30.0000 chunk 169 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 130 optimal weight: 40.0000 chunk 202 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** ** 10 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18404 Z= 0.313 Angle : 0.591 6.851 24955 Z= 0.300 Chirality : 0.041 0.152 2805 Planarity : 0.004 0.064 3164 Dihedral : 12.318 165.383 2771 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.87 % Allowed : 25.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2228 helix: 1.29 (0.19), residues: 792 sheet: -0.45 (0.24), residues: 512 loop : -0.71 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 2 158 HIS 0.005 0.001 HIS 5 27 PHE 0.019 0.001 PHE 2 230 TYR 0.018 0.001 TYR 1 912 ARG 0.004 0.000 ARG 6 73 *********************** 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 184 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 93 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 726 MET cc_start: 0.8110 (tpp) cc_final: 0.7847 (tpp) REVERT: 2 19 MET cc_start: 0.9464 (mmm) cc_final: 0.9241 (mmm) REVERT: 2 254 MET cc_start: 0.9231 (mtp) cc_final: 0.8818 (mmm) REVERT: 3 130 MET cc_start: 0.8569 (mmm) cc_final: 0.8299 (mmm) REVERT: 3 251 MET cc_start: 0.8776 (tpp) cc_final: 0.7910 (tmm) REVERT: 7 165 MET cc_start: 0.5110 (mpp) cc_final: 0.4582 (tmm) REVERT: 8 14 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8472 (mmp) REVERT: 8 71 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9430 (pp) REVERT: 8 85 HIS cc_start: 0.9327 (OUTLIER) cc_final: 0.8869 (m90) outliers start: 91 outliers final: 45 residues processed: 171 average time/residue: 0.2358 time to fit residues: 67.3172 Evaluate side-chains 137 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 89 time to evaluate : 2.216 ------------------------------------------------------------------------------- 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 107 MET Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 340 ASN Chi-restraints excluded: chain 1 residue 425 THR Chi-restraints excluded: chain 1 residue 452 VAL Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 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 34 VAL Chi-restraints excluded: chain 2 residue 52 ILE Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 160 THR Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 165 LEU Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 5 residue 69 ASP Chi-restraints excluded: chain 5 residue 78 ASN Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 8 residue 14 MET 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 64 ASP Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 219 optimal weight: 0.0060 chunk 180 optimal weight: 0.9990 chunk 201 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- 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 1 775 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18404 Z= 0.252 Angle : 0.563 6.912 24955 Z= 0.284 Chirality : 0.041 0.163 2805 Planarity : 0.004 0.055 3164 Dihedral : 11.811 162.925 2759 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.55 % Allowed : 25.91 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2228 helix: 1.28 (0.19), residues: 800 sheet: -0.37 (0.24), residues: 510 loop : -0.69 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP 2 158 HIS 0.003 0.001 HIS 1 580 PHE 0.015 0.001 PHE 2 230 TYR 0.014 0.001 TYR 1 943 ARG 0.003 0.000 ARG 6 73 *********************** 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 176 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 91 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 726 MET cc_start: 0.8044 (tpp) cc_final: 0.7566 (tpp) REVERT: 2 226 MET cc_start: 0.8010 (ppp) cc_final: 0.7622 (ppp) REVERT: 2 254 MET cc_start: 0.9237 (mtp) cc_final: 0.8801 (mmm) REVERT: 3 251 MET cc_start: 0.8768 (tpp) cc_final: 0.7888 (tmm) REVERT: 7 162 MET cc_start: 0.8013 (pmm) cc_final: 0.7579 (pmm) REVERT: 7 165 MET cc_start: 0.5424 (mpp) cc_final: 0.4855 (tmm) REVERT: 8 14 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8328 (mmp) REVERT: 8 85 HIS cc_start: 0.9316 (OUTLIER) cc_final: 0.8835 (m90) REVERT: 8 134 MET cc_start: 0.8579 (mmm) cc_final: 0.8215 (mmt) outliers start: 85 outliers final: 55 residues processed: 163 average time/residue: 0.2418 time to fit residues: 66.3213 Evaluate side-chains 144 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 87 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 340 ASN Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 452 VAL Chi-restraints excluded: chain 1 residue 463 THR Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 577 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 757 ILE Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 775 GLN Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 978 ILE Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 34 VAL Chi-restraints excluded: chain 2 residue 52 ILE Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 3 residue 12 ILE Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 160 THR 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 56 THR Chi-restraints excluded: chain 5 residue 69 ASP Chi-restraints excluded: chain 5 residue 78 ASN Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 6 residue 44 LEU Chi-restraints excluded: chain 6 residue 49 LEU Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 8 residue 14 MET Chi-restraints excluded: chain 8 residue 78 ILE Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 64 ASP 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 200 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 192 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 196 HIS ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 269 GLN ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 18404 Z= 0.551 Angle : 0.725 8.629 24955 Z= 0.365 Chirality : 0.044 0.193 2805 Planarity : 0.005 0.050 3164 Dihedral : 11.603 163.191 2759 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 7.07 % Allowed : 25.05 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2228 helix: 1.07 (0.18), residues: 803 sheet: -0.72 (0.23), residues: 516 loop : -0.91 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP 2 158 HIS 0.007 0.002 HIS 1 783 PHE 0.015 0.002 PHE 2 230 TYR 0.029 0.002 TYR 1 943 ARG 0.004 0.000 ARG 7 66 *********************** 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 219 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 87 time to evaluate : 2.076 Fit side-chains revert: symmetry clash REVERT: 1 257 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8254 (ptm-80) REVERT: 1 331 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.8897 (p) REVERT: 2 158 TRP cc_start: 0.8774 (OUTLIER) cc_final: 0.8539 (m-10) REVERT: 2 226 MET cc_start: 0.7981 (ppp) cc_final: 0.7668 (ppp) REVERT: 2 254 MET cc_start: 0.9255 (mtp) cc_final: 0.8817 (mmm) REVERT: 3 251 MET cc_start: 0.8891 (tpp) cc_final: 0.7997 (tmm) REVERT: 7 165 MET cc_start: 0.5579 (mpp) cc_final: 0.4878 (tmm) REVERT: 8 14 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.9048 (mmp) REVERT: 8 16 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8729 (mm) REVERT: 8 85 HIS cc_start: 0.9401 (OUTLIER) cc_final: 0.8909 (m90) outliers start: 132 outliers final: 93 residues processed: 205 average time/residue: 0.2267 time to fit residues: 77.1901 Evaluate side-chains 183 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 84 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 107 MET Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 146 LEU Chi-restraints excluded: chain 1 residue 191 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 257 ARG Chi-restraints excluded: chain 1 residue 276 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 340 ASN Chi-restraints excluded: chain 1 residue 372 THR Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 425 THR Chi-restraints excluded: chain 1 residue 452 VAL Chi-restraints excluded: chain 1 residue 463 THR Chi-restraints excluded: chain 1 residue 522 ILE Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 577 THR Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 757 ILE Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 775 GLN Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 784 ILE Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 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 942 ILE Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 965 ILE Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 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 52 ILE 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 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 230 PHE 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 160 THR Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 3 residue 249 GLU Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 4 residue 162 SER Chi-restraints excluded: chain 4 residue 165 LEU Chi-restraints excluded: chain 5 residue 56 THR Chi-restraints excluded: chain 5 residue 69 ASP Chi-restraints excluded: chain 5 residue 73 THR Chi-restraints excluded: chain 5 residue 78 ASN Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 29 CYS Chi-restraints excluded: chain 6 residue 31 THR Chi-restraints excluded: chain 6 residue 34 SER Chi-restraints excluded: chain 6 residue 44 LEU Chi-restraints excluded: chain 6 residue 49 LEU Chi-restraints excluded: chain 6 residue 53 ILE Chi-restraints excluded: chain 6 residue 56 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 86 THR Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 8 residue 14 MET Chi-restraints excluded: chain 8 residue 16 LEU Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 8 residue 78 ILE Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 64 ASP Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 253 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18404 Z= 0.167 Angle : 0.562 7.638 24955 Z= 0.283 Chirality : 0.041 0.186 2805 Planarity : 0.004 0.051 3164 Dihedral : 11.045 162.614 2759 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.28 % Allowed : 27.30 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2228 helix: 1.27 (0.19), residues: 799 sheet: -0.42 (0.24), residues: 484 loop : -0.72 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 2 158 HIS 0.005 0.001 HIS 1 580 PHE 0.014 0.001 PHE 2 230 TYR 0.014 0.001 TYR 8 93 ARG 0.003 0.000 ARG 2 142 *********************** 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 167 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 87 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: 1 726 MET cc_start: 0.7823 (tpp) cc_final: 0.7616 (tpp) REVERT: 2 254 MET cc_start: 0.9251 (mtp) cc_final: 0.8795 (mmm) REVERT: 3 251 MET cc_start: 0.8835 (tpp) cc_final: 0.7962 (tmm) REVERT: 7 118 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7925 (ppp) REVERT: 7 165 MET cc_start: 0.5327 (mpp) cc_final: 0.4756 (tmm) REVERT: 8 16 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8678 (mm) REVERT: 8 85 HIS cc_start: 0.9315 (OUTLIER) cc_final: 0.8834 (m90) outliers start: 80 outliers final: 49 residues processed: 157 average time/residue: 0.2618 time to fit residues: 68.4102 Evaluate side-chains 134 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 82 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE 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 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 340 ASN Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 425 THR Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR 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 138 VAL Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 12 ILE 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 12 ILE Chi-restraints excluded: chain 5 residue 56 THR Chi-restraints excluded: chain 5 residue 69 ASP Chi-restraints excluded: chain 5 residue 78 ASN Chi-restraints excluded: chain 6 residue 36 LEU Chi-restraints excluded: chain 6 residue 44 LEU Chi-restraints excluded: chain 6 residue 49 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 118 MET Chi-restraints excluded: chain 8 residue 16 LEU Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 64 ASP Chi-restraints excluded: chain 10 residue 85 LEU Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 173 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** ** 1 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 253 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.118 18404 Z= 0.584 Angle : 0.751 9.685 24955 Z= 0.378 Chirality : 0.045 0.196 2805 Planarity : 0.005 0.052 3164 Dihedral : 11.090 164.494 2759 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 6.32 % Allowed : 25.91 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2228 helix: 0.96 (0.18), residues: 801 sheet: -0.68 (0.23), residues: 504 loop : -0.92 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP 2 158 HIS 0.008 0.002 HIS 1 783 PHE 0.016 0.002 PHE 2 230 TYR 0.030 0.002 TYR 1 943 ARG 0.004 0.001 ARG 7 66 *********************** 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 202 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 84 time to evaluate : 2.349 Fit side-chains revert: symmetry clash REVERT: 1 331 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8908 (p) REVERT: 1 726 MET cc_start: 0.8187 (tpp) cc_final: 0.7701 (tpp) REVERT: 2 254 MET cc_start: 0.9267 (mtp) cc_final: 0.8818 (mmm) REVERT: 3 130 MET cc_start: 0.8534 (mmm) cc_final: 0.8150 (mmm) REVERT: 3 251 MET cc_start: 0.8907 (tpp) cc_final: 0.8026 (tmm) REVERT: 7 118 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8174 (ppp) outliers start: 118 outliers final: 95 residues processed: 189 average time/residue: 0.2277 time to fit residues: 72.1289 Evaluate side-chains 178 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 81 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 107 MET Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 167 LEU Chi-restraints excluded: chain 1 residue 191 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 259 ILE Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 302 LEU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 340 ASN Chi-restraints excluded: chain 1 residue 372 THR Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 425 THR Chi-restraints excluded: chain 1 residue 463 THR Chi-restraints excluded: chain 1 residue 522 ILE Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 577 THR Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 761 LEU Chi-restraints excluded: chain 1 residue 769 ILE Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 784 ILE Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 823 SER Chi-restraints excluded: chain 1 residue 851 ILE 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 942 ILE 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 52 ILE Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 12 ILE Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 160 THR 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 12 ILE Chi-restraints excluded: chain 5 residue 56 THR Chi-restraints excluded: chain 5 residue 69 ASP Chi-restraints excluded: chain 5 residue 73 THR Chi-restraints excluded: chain 5 residue 78 ASN Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 31 THR Chi-restraints excluded: chain 6 residue 49 LEU Chi-restraints excluded: chain 6 residue 53 ILE Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 86 THR Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 60 ASP 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 7 residue 140 MET Chi-restraints excluded: chain 7 residue 151 LYS Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 8 residue 60 LEU Chi-restraints excluded: chain 8 residue 78 ILE Chi-restraints excluded: chain 8 residue 182 THR Chi-restraints excluded: chain 10 residue 64 ASP Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 152 VAL Chi-restraints excluded: chain 10 residue 173 VAL Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 187 LEU Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 214 optimal weight: 0.9980 chunk 134 optimal weight: 0.0770 chunk 131 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 18404 Z= 0.165 Angle : 0.584 9.518 24955 Z= 0.292 Chirality : 0.041 0.147 2805 Planarity : 0.004 0.054 3164 Dihedral : 10.614 164.442 2759 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.53 % Allowed : 28.53 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2228 helix: 1.19 (0.19), residues: 798 sheet: -0.37 (0.24), residues: 476 loop : -0.68 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP 2 158 HIS 0.006 0.001 HIS 1 580 PHE 0.015 0.001 PHE 2 230 TYR 0.014 0.001 TYR 7 136 ARG 0.004 0.000 ARG10 204 *********************** 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 153 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 87 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 726 MET cc_start: 0.7987 (tpp) cc_final: 0.7523 (tpp) REVERT: 2 183 MET cc_start: 0.8926 (mtp) cc_final: 0.8671 (mtm) REVERT: 2 254 MET cc_start: 0.9235 (mtp) cc_final: 0.8790 (mmm) REVERT: 3 251 MET cc_start: 0.8837 (tpp) cc_final: 0.7967 (tmm) REVERT: 7 118 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8082 (ppp) REVERT: 7 165 MET cc_start: 0.5299 (mpp) cc_final: 0.4878 (tmm) REVERT: 8 85 HIS cc_start: 0.9314 (OUTLIER) cc_final: 0.8819 (m90) outliers start: 66 outliers final: 46 residues processed: 144 average time/residue: 0.2474 time to fit residues: 60.5543 Evaluate side-chains 132 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 84 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 56 VAL 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 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 340 ASN Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 436 LEU Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 775 GLN Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 52 ILE Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 12 ILE 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 12 ILE Chi-restraints excluded: chain 5 residue 56 THR Chi-restraints excluded: chain 5 residue 69 ASP Chi-restraints excluded: chain 5 residue 78 ASN Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 6 residue 34 SER Chi-restraints excluded: chain 6 residue 49 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 118 MET Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 112 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 146 optimal weight: 30.0000 chunk 106 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 168 optimal weight: 7.9990 chunk 195 optimal weight: 0.9980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** ** 1 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18404 Z= 0.218 Angle : 0.578 9.897 24955 Z= 0.290 Chirality : 0.041 0.157 2805 Planarity : 0.004 0.056 3164 Dihedral : 10.413 165.059 2759 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.32 % Allowed : 28.75 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2228 helix: 1.22 (0.19), residues: 797 sheet: -0.40 (0.24), residues: 481 loop : -0.69 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP 2 158 HIS 0.004 0.001 HIS 1 580 PHE 0.021 0.001 PHE 2 230 TYR 0.013 0.001 TYR 7 136 ARG 0.003 0.000 ARG10 204 *********************** 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 149 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 87 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 726 MET cc_start: 0.8104 (tpp) cc_final: 0.7630 (tpp) REVERT: 2 254 MET cc_start: 0.9267 (mtp) cc_final: 0.8837 (mmm) REVERT: 3 251 MET cc_start: 0.8846 (tpp) cc_final: 0.7921 (tmm) REVERT: 7 118 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8118 (ppp) REVERT: 7 165 MET cc_start: 0.5390 (mpp) cc_final: 0.4936 (tmm) REVERT: 8 134 MET cc_start: 0.8981 (mmm) cc_final: 0.8761 (mmt) outliers start: 62 outliers final: 52 residues processed: 140 average time/residue: 0.2399 time to fit residues: 56.7833 Evaluate side-chains 137 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 84 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 340 ASN Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 425 THR Chi-restraints excluded: chain 1 residue 436 LEU Chi-restraints excluded: chain 1 residue 463 THR Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 577 THR Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR 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 52 ILE Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 12 ILE 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 56 THR Chi-restraints excluded: chain 5 residue 69 ASP Chi-restraints excluded: chain 5 residue 73 THR Chi-restraints excluded: chain 5 residue 78 ASN Chi-restraints excluded: chain 6 residue 34 SER Chi-restraints excluded: chain 6 residue 44 LEU Chi-restraints excluded: chain 6 residue 49 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 118 MET Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 10 residue 64 ASP Chi-restraints excluded: chain 10 residue 112 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 overall best weight: 2.6984 ------------------------------------------------------------------------------- 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** ** 1 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18404 Z= 0.266 Angle : 0.593 9.067 24955 Z= 0.296 Chirality : 0.041 0.152 2805 Planarity : 0.004 0.057 3164 Dihedral : 10.248 166.281 2759 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.75 % Allowed : 28.27 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2228 helix: 1.23 (0.19), residues: 798 sheet: -0.42 (0.24), residues: 494 loop : -0.68 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP 2 158 HIS 0.005 0.001 HIS 1 580 PHE 0.020 0.001 PHE 2 230 TYR 0.016 0.001 TYR 7 136 ARG 0.005 0.000 ARG10 204 *********************** 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 155 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 85 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 726 MET cc_start: 0.8110 (tpp) cc_final: 0.7737 (tpp) REVERT: 2 254 MET cc_start: 0.9266 (mtp) cc_final: 0.8836 (mmm) REVERT: 3 251 MET cc_start: 0.8851 (tpp) cc_final: 0.7937 (tmm) REVERT: 7 118 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8164 (ppp) REVERT: 7 165 MET cc_start: 0.5473 (mpp) cc_final: 0.4939 (tmm) outliers start: 70 outliers final: 61 residues processed: 147 average time/residue: 0.2458 time to fit residues: 60.8040 Evaluate side-chains 146 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 84 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 340 ASN Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 425 THR Chi-restraints excluded: chain 1 residue 436 LEU Chi-restraints excluded: chain 1 residue 463 THR Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 577 THR Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 823 SER Chi-restraints excluded: chain 1 residue 851 ILE 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 968 VAL Chi-restraints excluded: chain 1 residue 972 LEU Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 52 ILE Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 12 ILE Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 160 THR 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 56 THR Chi-restraints excluded: chain 5 residue 69 ASP Chi-restraints excluded: chain 5 residue 73 THR Chi-restraints excluded: chain 5 residue 78 ASN Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 34 SER Chi-restraints excluded: chain 6 residue 49 LEU Chi-restraints excluded: chain 6 residue 67 ILE 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 118 MET Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 10 residue 64 ASP Chi-restraints excluded: chain 10 residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 147 optimal weight: 0.0670 chunk 222 optimal weight: 5.9990 chunk 204 optimal weight: 0.0270 chunk 176 optimal weight: 7.9990 chunk 18 optimal weight: 0.0980 chunk 136 optimal weight: 0.2980 chunk 108 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18404 Z= 0.156 Angle : 0.587 12.684 24955 Z= 0.291 Chirality : 0.041 0.150 2805 Planarity : 0.004 0.059 3164 Dihedral : 9.945 166.668 2759 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.52 % Allowed : 29.60 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2228 helix: 1.23 (0.19), residues: 793 sheet: -0.15 (0.25), residues: 485 loop : -0.57 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP 2 158 HIS 0.004 0.001 HIS 1 580 PHE 0.022 0.001 PHE 2 230 TYR 0.015 0.001 TYR 1 672 ARG 0.005 0.000 ARG 5 102 ********************** 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 138 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 91 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 293 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9543 (tt) REVERT: 1 726 MET cc_start: 0.8041 (tpp) cc_final: 0.7675 (tpp) REVERT: 2 183 MET cc_start: 0.8875 (mtm) cc_final: 0.8666 (mtm) REVERT: 2 254 MET cc_start: 0.9272 (mtp) cc_final: 0.8840 (mmm) REVERT: 3 251 MET cc_start: 0.8791 (tpp) cc_final: 0.7913 (tmm) REVERT: 7 118 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8157 (ppp) REVERT: 7 165 MET cc_start: 0.5337 (mpp) cc_final: 0.4910 (tmm) REVERT: 8 134 MET cc_start: 0.8452 (mmt) cc_final: 0.7079 (tpp) outliers start: 47 outliers final: 40 residues processed: 132 average time/residue: 0.2433 time to fit residues: 54.5490 Evaluate side-chains 129 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 87 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 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 425 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 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 823 SER Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 972 LEU Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 12 ILE 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 56 THR Chi-restraints excluded: chain 5 residue 69 ASP Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 6 residue 49 LEU Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 118 MET Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 10 residue 64 ASP Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 20.0000 chunk 54 optimal weight: 0.0030 chunk 163 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 177 optimal weight: 0.0370 chunk 74 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 overall best weight: 1.2070 ------------------------------------------------------------------------------- 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** ** 1 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 265 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 = 0.3502 r_free = 0.3502 target = 0.051766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.035106 restraints weight = 108296.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.036391 restraints weight = 48866.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.037199 restraints weight = 31971.545| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18404 Z= 0.176 Angle : 0.570 9.545 24955 Z= 0.283 Chirality : 0.040 0.145 2805 Planarity : 0.004 0.055 3164 Dihedral : 9.827 167.691 2759 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.19 % Allowed : 29.98 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2228 helix: 1.28 (0.19), residues: 796 sheet: -0.21 (0.24), residues: 508 loop : -0.51 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP 2 158 HIS 0.003 0.001 HIS 1 580 PHE 0.021 0.001 PHE 2 230 TYR 0.014 0.001 TYR 7 136 ARG 0.005 0.000 ARG 2 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.64 seconds wall clock time: 57 minutes 57.30 seconds (3477.30 seconds total)