Starting phenix.real_space_refine on Wed Sep 25 10:29:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/09_2024/8bpr_16164.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/09_2024/8bpr_16164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/09_2024/8bpr_16164.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/09_2024/8bpr_16164.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/09_2024/8bpr_16164.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/09_2024/8bpr_16164.cif" } resolution = 3.65 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= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 48 5.49 5 Mg 2 5.21 5 S 19 5.16 5 C 6066 2.51 5 N 1944 2.21 5 O 1973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10055 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2692 Chain: "B" Number of atoms: 2643 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2635 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 340, 2635 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2673 Chain: "C" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 203 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 774 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 558 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 245 Chain: "E" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 861 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 488 Unresolved non-hydrogen angles: 622 Unresolved non-hydrogen dihedrals: 389 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 24, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 262 Chain: "F" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1005 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 945 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain breaks: 4 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 578 Unresolved non-hydrogen angles: 741 Unresolved non-hydrogen dihedrals: 477 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 294 Chain: "X" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5739 SG CYS D 55 43.572 87.803 58.251 1.00187.00 S ATOM 5755 SG CYS D 58 40.684 86.789 56.482 1.00186.50 S ATOM 5799 SG CYS D 67 43.623 86.075 55.256 1.00198.45 S ATOM 5815 SG CYS D 70 41.299 88.973 54.452 1.00194.96 S ATOM 6485 SG CYS E 55 18.226 31.458 61.849 1.00388.72 S ATOM 6501 SG CYS E 58 19.386 34.024 62.778 1.00384.50 S ATOM 6545 SG CYS E 67 17.483 33.088 65.781 1.00324.74 S ATOM 6561 SG CYS E 70 15.165 33.476 63.024 1.00332.08 S ATOM 7380 SG CYS F 55 68.613 12.947 73.407 1.00115.77 S ATOM 7396 SG CYS F 58 68.887 15.480 74.630 1.00 97.49 S ATOM 7440 SG CYS F 67 69.461 16.970 72.486 1.00131.47 S ATOM 7456 SG CYS F 70 72.318 14.522 72.967 1.00134.38 S Time building chain proxies: 9.85, per 1000 atoms: 0.98 Number of scatterers: 10055 At special positions: 0 Unit cell: (96.32, 100.62, 165.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 19 16.00 P 48 15.00 Mg 2 11.99 O 1973 8.00 N 1944 7.00 C 6066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 67 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 55 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 58 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 67 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 70 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 58 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 67 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 70 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 58 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 55 " Number of angles added : 18 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 13 sheets defined 52.5% alpha, 14.1% beta 11 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.173A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.680A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 163 removed outlier: 3.976A pdb=" N ALA A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 202 removed outlier: 3.896A pdb=" N TYR A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.512A pdb=" N ASP A 245 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'B' and resid 35 through 47 removed outlier: 3.541A pdb=" N LEU B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.876A pdb=" N LEU B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 141 through 163 removed outlier: 3.947A pdb=" N ALA B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 205 removed outlier: 4.061A pdb=" N GLU B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 241 through 245 removed outlier: 3.530A pdb=" N ASP B 245 " --> pdb=" O PRO B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 Processing helix chain 'B' and resid 261 through 285 Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 35 through 48 Processing helix chain 'D' and resid 5 through 17 removed outlier: 4.300A pdb=" N LYS D 9 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 34 removed outlier: 3.852A pdb=" N PHE D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 47 removed outlier: 4.503A pdb=" N GLU D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 142 through 153 Processing helix chain 'D' and resid 175 through 179 removed outlier: 3.767A pdb=" N ALA D 179 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'E' and resid 10 through 17 removed outlier: 3.615A pdb=" N LEU E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 35 Processing helix chain 'E' and resid 35 through 50 Processing helix chain 'E' and resid 85 through 96 Processing helix chain 'E' and resid 110 through 114 Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 142 through 159 Processing helix chain 'E' and resid 180 through 190 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 21 through 35 Processing helix chain 'F' and resid 36 through 47 removed outlier: 3.836A pdb=" N GLU F 40 " --> pdb=" O LYS F 36 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 96 removed outlier: 3.772A pdb=" N SER F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 160 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.925A pdb=" N GLU G 91 " --> pdb=" O HIS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 114 through 132 Proline residue: G 120 - end of helix Processing helix chain 'G' and resid 135 through 150 removed outlier: 3.516A pdb=" N ARG G 145 " --> pdb=" O TRP G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 189 removed outlier: 3.545A pdb=" N GLY G 179 " --> pdb=" O LEU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 199 Proline residue: G 196 - end of helix Processing helix chain 'G' and resid 206 through 219 Processing helix chain 'G' and resid 221 through 226 removed outlier: 3.941A pdb=" N GLU G 225 " --> pdb=" O ARG G 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 9 removed outlier: 5.337A pdb=" N LEU A 3 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 73 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 113 removed outlier: 3.600A pdb=" N LEU A 319 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N CYS A 331 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 27 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 333 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 29 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 4.400A pdb=" N VAL A 92 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 97 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.613A pdb=" N ASP A 246 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 9 removed outlier: 6.137A pdb=" N LEU B 3 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU B 73 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 93 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 113 removed outlier: 6.186A pdb=" N VAL B 111 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASP B 293 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 113 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 290 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY B 24 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU B 319 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER B 26 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLY B 321 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU B 28 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N CYS B 331 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA B 27 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL B 333 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 29 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 214 removed outlier: 3.533A pdb=" N ASP B 246 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 100 through 101 removed outlier: 7.166A pdb=" N ASP D 76 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N GLU D 134 " --> pdb=" O ASP D 76 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER D 78 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL D 136 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 80 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL D 135 " --> pdb=" O THR D 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 192 through 193 removed outlier: 6.046A pdb=" N VAL E 135 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU E 80 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ALA E 138 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL E 82 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS E 103 " --> pdb=" O ALA E 81 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL E 83 " --> pdb=" O HIS E 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.673A pdb=" N ARG F 53 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 101 through 104 removed outlier: 6.135A pdb=" N ALA F 81 " --> pdb=" O HIS F 103 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU F 80 " --> pdb=" O VAL F 136 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 15 through 24 removed outlier: 6.362A pdb=" N VAL G 19 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL G 35 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU G 78 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL G 44 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N GLN G 80 " --> pdb=" O VAL G 44 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN G 67 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA G 81 " --> pdb=" O ARG G 65 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG G 65 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU G 83 " --> pdb=" O HIS G 63 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N HIS G 63 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 167 through 169 removed outlier: 3.560A pdb=" N LEU G 163 " --> pdb=" O VAL G 173 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL G 173 " --> pdb=" O LEU G 163 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3129 1.34 - 1.45: 1455 1.45 - 1.57: 5550 1.57 - 1.69: 94 1.69 - 1.81: 22 Bond restraints: 10250 Sorted by residual: bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.629 0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O5' ANP B 901 " pdb=" PA ANP B 901 " ideal model delta sigma weight residual 1.655 1.593 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 10245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 14022 2.20 - 4.40: 104 4.40 - 6.60: 13 6.60 - 8.80: 5 8.80 - 11.01: 2 Bond angle restraints: 14146 Sorted by residual: angle pdb=" O1B ANP A 901 " pdb=" PB ANP A 901 " pdb=" O3A ANP A 901 " ideal model delta sigma weight residual 103.40 114.41 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O3A ANP B 901 " ideal model delta sigma weight residual 103.40 114.37 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" PA ANP A 901 " pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 125.41 133.35 -7.94 3.00e+00 1.11e-01 7.01e+00 angle pdb=" PA ANP B 901 " pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 125.41 133.13 -7.72 3.00e+00 1.11e-01 6.61e+00 angle pdb=" CB LYS F 118 " pdb=" CG LYS F 118 " pdb=" CD LYS F 118 " ideal model delta sigma weight residual 111.30 117.18 -5.88 2.30e+00 1.89e-01 6.53e+00 ... (remaining 14141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5287 17.95 - 35.89: 440 35.89 - 53.84: 235 53.84 - 71.79: 28 71.79 - 89.73: 10 Dihedral angle restraints: 6000 sinusoidal: 2060 harmonic: 3940 Sorted by residual: dihedral pdb=" CA ALA E 167 " pdb=" C ALA E 167 " pdb=" N TYR E 168 " pdb=" CA TYR E 168 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLU D 133 " pdb=" C GLU D 133 " pdb=" N GLU D 134 " pdb=" CA GLU D 134 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ARG D 127 " pdb=" C ARG D 127 " pdb=" N ARG D 128 " pdb=" CA ARG D 128 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1505 0.057 - 0.113: 166 0.113 - 0.170: 4 0.170 - 0.227: 0 0.227 - 0.283: 2 Chirality restraints: 1677 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA VAL F 161 " pdb=" N VAL F 161 " pdb=" C VAL F 161 " pdb=" CB VAL F 161 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 1674 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 88 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C ASP E 88 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP E 88 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU E 89 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 114 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO A 115 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 123 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 124 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.017 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 60 2.64 - 3.20: 8305 3.20 - 3.77: 14384 3.77 - 4.33: 17909 4.33 - 4.90: 29849 Nonbonded interactions: 70507 Sorted by model distance: nonbonded pdb=" O2G ANP B 901 " pdb="MG MG B 902 " model vdw 2.072 2.170 nonbonded pdb=" OG1 THR B 37 " pdb="MG MG B 902 " model vdw 2.078 2.170 nonbonded pdb=" O1B ANP B 901 " pdb="MG MG B 902 " model vdw 2.115 2.170 nonbonded pdb=" O1B ANP A 901 " pdb="MG MG A 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G ANP A 901 " pdb="MG MG A 902 " model vdw 2.145 2.170 ... (remaining 70502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 51 or resid 53 through 72 or (resid 73 and (name \ N or name CA or name C or name O or name CB )) or resid 74 through 96 or (resid \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 through \ 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) or r \ esid 142 through 165 or (resid 166 and (name N or name CA or name C or name O or \ name CB )) or resid 167 through 191 or resid 193 through 197 or resid 199 throu \ gh 341 or resid 901 through 902)) selection = (chain 'B' and (resid 1 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 191 or resid 193 through 197 or res \ id 199 through 285 or (resid 286 and (name N or name CA or name C or name O or n \ ame CB )) or resid 287 through 341 or resid 901 through 902)) } ncs_group { reference = (chain 'D' and (resid 9 through 18 or resid 22 through 71 or resid 77 through 19 \ 4 or resid 201)) selection = (chain 'E' and (resid 9 through 48 or resid 54 through 102 or resid 122 through \ 153 or resid 162 through 194 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 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: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.150 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.004 0.166 10250 Z= 0.209 Angle : 0.509 11.006 14146 Z= 0.253 Chirality : 0.036 0.283 1677 Planarity : 0.003 0.031 1745 Dihedral : 17.505 89.732 3460 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.66 % Allowed : 0.00 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1359 helix: 1.80 (0.21), residues: 638 sheet: 0.54 (0.37), residues: 193 loop : -0.96 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.003 0.001 HIS A 277 PHE 0.007 0.001 PHE B 6 TYR 0.004 0.001 TYR B 178 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.7231 (m-40) cc_final: 0.6879 (t0) REVERT: A 34 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7380 (mp10) REVERT: A 55 LEU cc_start: 0.8863 (tp) cc_final: 0.8516 (tp) REVERT: B 131 TYR cc_start: 0.8732 (t80) cc_final: 0.8480 (t80) REVERT: F 129 LEU cc_start: 0.8463 (mm) cc_final: 0.8256 (tp) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.3354 time to fit residues: 73.2982 Evaluate side-chains 96 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 50.0000 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 128 optimal weight: 40.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10250 Z= 0.272 Angle : 0.607 10.665 14146 Z= 0.313 Chirality : 0.040 0.160 1677 Planarity : 0.004 0.035 1745 Dihedral : 16.965 89.039 2012 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.98 % Allowed : 11.09 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1359 helix: 2.40 (0.21), residues: 655 sheet: 0.76 (0.37), residues: 195 loop : -0.94 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 171 HIS 0.006 0.002 HIS A 257 PHE 0.018 0.002 PHE A 259 TYR 0.018 0.002 TYR F 102 ARG 0.007 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8520 (mp0) cc_final: 0.8211 (mp0) REVERT: B 131 TYR cc_start: 0.8858 (t80) cc_final: 0.8504 (t80) REVERT: F 90 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6829 (m-80) REVERT: F 94 ARG cc_start: 0.8984 (ptm-80) cc_final: 0.8752 (ttp80) REVERT: F 129 LEU cc_start: 0.8532 (mm) cc_final: 0.8186 (tt) REVERT: F 144 GLU cc_start: 0.8430 (mp0) cc_final: 0.8207 (mt-10) outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.2459 time to fit residues: 34.3824 Evaluate side-chains 88 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10250 Z= 0.328 Angle : 0.628 10.711 14146 Z= 0.319 Chirality : 0.041 0.143 1677 Planarity : 0.005 0.047 1745 Dihedral : 16.934 85.760 2012 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.81 % Allowed : 13.08 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1359 helix: 2.53 (0.20), residues: 659 sheet: 0.86 (0.37), residues: 190 loop : -1.05 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 295 HIS 0.008 0.002 HIS A 257 PHE 0.032 0.003 PHE F 126 TYR 0.018 0.002 TYR F 102 ARG 0.007 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8500 (mm-40) cc_final: 0.7719 (mp10) REVERT: B 131 TYR cc_start: 0.8971 (t80) cc_final: 0.8432 (t80) REVERT: F 90 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: F 115 ILE cc_start: 0.9211 (mp) cc_final: 0.8794 (tt) REVERT: F 129 LEU cc_start: 0.8557 (mm) cc_final: 0.8171 (tp) REVERT: F 144 GLU cc_start: 0.8648 (mp0) cc_final: 0.8364 (mt-10) outliers start: 20 outliers final: 14 residues processed: 87 average time/residue: 0.2442 time to fit residues: 29.4891 Evaluate side-chains 83 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 40.0000 chunk 97 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 137 optimal weight: 40.0000 chunk 122 optimal weight: 50.0000 chunk 36 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10250 Z= 0.251 Angle : 0.550 9.026 14146 Z= 0.282 Chirality : 0.038 0.143 1677 Planarity : 0.004 0.042 1745 Dihedral : 16.699 88.002 2012 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.15 % Allowed : 15.23 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.23), residues: 1359 helix: 2.77 (0.20), residues: 659 sheet: 0.66 (0.36), residues: 193 loop : -0.96 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 105 HIS 0.006 0.002 HIS B 277 PHE 0.017 0.001 PHE A 259 TYR 0.015 0.001 TYR A 19 ARG 0.004 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7546 (mp10) REVERT: A 237 GLN cc_start: 0.9245 (mt0) cc_final: 0.8642 (mt0) REVERT: B 131 TYR cc_start: 0.8980 (t80) cc_final: 0.8381 (t80) REVERT: B 312 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8639 (tm-30) REVERT: F 90 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6932 (m-80) REVERT: F 115 ILE cc_start: 0.9234 (mp) cc_final: 0.8801 (tt) REVERT: F 129 LEU cc_start: 0.8601 (mm) cc_final: 0.8245 (tt) REVERT: F 144 GLU cc_start: 0.8664 (mp0) cc_final: 0.8349 (mt-10) outliers start: 16 outliers final: 10 residues processed: 82 average time/residue: 0.2513 time to fit residues: 28.8099 Evaluate side-chains 77 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 40.0000 chunk 0 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 123 optimal weight: 50.0000 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10250 Z= 0.479 Angle : 0.705 9.021 14146 Z= 0.359 Chirality : 0.043 0.278 1677 Planarity : 0.005 0.045 1745 Dihedral : 16.985 93.223 2012 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.14 % Allowed : 16.06 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1359 helix: 2.49 (0.20), residues: 657 sheet: 0.33 (0.35), residues: 207 loop : -1.10 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 295 HIS 0.011 0.003 HIS B 277 PHE 0.033 0.003 PHE A 259 TYR 0.015 0.002 TYR A 150 ARG 0.007 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8478 (mm-40) cc_final: 0.7736 (mp10) REVERT: A 102 ARG cc_start: 0.8449 (mmt90) cc_final: 0.8248 (mmt90) REVERT: A 232 GLU cc_start: 0.8602 (tp30) cc_final: 0.8389 (tp30) REVERT: B 39 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8615 (tt) REVERT: B 312 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8574 (tm-30) REVERT: F 90 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6969 (m-80) REVERT: F 115 ILE cc_start: 0.9165 (mp) cc_final: 0.8721 (tt) REVERT: F 129 LEU cc_start: 0.8620 (mm) cc_final: 0.8170 (tp) outliers start: 22 outliers final: 16 residues processed: 82 average time/residue: 0.2345 time to fit residues: 27.2368 Evaluate side-chains 80 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 50.0000 chunk 27 optimal weight: 0.5980 chunk 80 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 137 optimal weight: 50.0000 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10250 Z= 0.203 Angle : 0.567 12.731 14146 Z= 0.283 Chirality : 0.038 0.180 1677 Planarity : 0.004 0.047 1745 Dihedral : 16.696 89.422 2012 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.15 % Allowed : 18.21 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1359 helix: 2.77 (0.20), residues: 663 sheet: 0.42 (0.35), residues: 206 loop : -0.94 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 105 HIS 0.005 0.001 HIS B 284 PHE 0.012 0.001 PHE A 259 TYR 0.010 0.001 TYR B 178 ARG 0.012 0.001 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8461 (mm-40) cc_final: 0.7553 (mp10) REVERT: A 119 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7973 (tp30) REVERT: A 232 GLU cc_start: 0.8771 (tp30) cc_final: 0.8453 (tp30) REVERT: B 131 TYR cc_start: 0.8980 (t80) cc_final: 0.8371 (t80) REVERT: B 312 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8590 (tm-30) REVERT: F 90 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: F 115 ILE cc_start: 0.9172 (mp) cc_final: 0.8748 (tt) REVERT: F 129 LEU cc_start: 0.8564 (mm) cc_final: 0.8175 (tp) outliers start: 16 outliers final: 10 residues processed: 74 average time/residue: 0.2431 time to fit residues: 25.1798 Evaluate side-chains 73 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 40.0000 chunk 100 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 85 optimal weight: 0.0980 chunk 83 optimal weight: 50.0000 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 10250 Z= 0.491 Angle : 0.697 10.217 14146 Z= 0.355 Chirality : 0.043 0.181 1677 Planarity : 0.005 0.044 1745 Dihedral : 16.916 94.317 2012 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.81 % Allowed : 18.21 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.23), residues: 1359 helix: 2.51 (0.20), residues: 662 sheet: 0.25 (0.36), residues: 198 loop : -1.03 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 105 HIS 0.012 0.003 HIS B 277 PHE 0.031 0.003 PHE A 259 TYR 0.016 0.002 TYR A 150 ARG 0.009 0.001 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8536 (mm-40) cc_final: 0.7862 (mp10) REVERT: A 119 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8045 (tm-30) REVERT: A 161 LEU cc_start: 0.8484 (tt) cc_final: 0.8241 (tt) REVERT: A 312 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8489 (tm-30) REVERT: B 39 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8644 (tt) REVERT: B 312 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8575 (tm-30) REVERT: F 90 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6950 (m-80) REVERT: F 129 LEU cc_start: 0.8660 (mm) cc_final: 0.8181 (tp) outliers start: 20 outliers final: 15 residues processed: 74 average time/residue: 0.2435 time to fit residues: 25.4168 Evaluate side-chains 73 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 56 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 87 optimal weight: 30.0000 chunk 93 optimal weight: 50.0000 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 131 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10250 Z= 0.179 Angle : 0.564 10.983 14146 Z= 0.280 Chirality : 0.038 0.199 1677 Planarity : 0.004 0.048 1745 Dihedral : 16.663 89.729 2012 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.65 % Allowed : 19.70 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1359 helix: 2.80 (0.20), residues: 664 sheet: 0.37 (0.36), residues: 207 loop : -0.86 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 105 HIS 0.008 0.001 HIS B 284 PHE 0.010 0.001 PHE A 259 TYR 0.009 0.001 TYR B 178 ARG 0.010 0.001 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7587 (mp10) REVERT: A 119 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7978 (tp30) REVERT: A 231 GLU cc_start: 0.8436 (pm20) cc_final: 0.8220 (pm20) REVERT: A 312 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8480 (tm-30) REVERT: B 39 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8618 (tt) REVERT: B 131 TYR cc_start: 0.8967 (t80) cc_final: 0.8320 (t80) REVERT: B 312 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8562 (tm-30) REVERT: F 90 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: F 118 LYS cc_start: 0.8956 (mmtm) cc_final: 0.8421 (ptmm) REVERT: F 129 LEU cc_start: 0.8628 (mm) cc_final: 0.8206 (tp) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.2368 time to fit residues: 23.9074 Evaluate side-chains 74 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 50.0000 chunk 127 optimal weight: 30.0000 chunk 131 optimal weight: 50.0000 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.073 10250 Z= 0.723 Angle : 0.861 10.198 14146 Z= 0.435 Chirality : 0.048 0.158 1677 Planarity : 0.006 0.052 1745 Dihedral : 17.190 99.923 2012 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.64 % Allowed : 18.05 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1359 helix: 2.22 (0.21), residues: 660 sheet: 0.01 (0.36), residues: 198 loop : -1.11 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 105 HIS 0.017 0.004 HIS A 283 PHE 0.044 0.004 PHE A 259 TYR 0.026 0.003 TYR A 150 ARG 0.014 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 55 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 173 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7663 (ttm110) REVERT: B 39 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8709 (tt) REVERT: F 90 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.7033 (m-80) REVERT: F 129 LEU cc_start: 0.8758 (mm) cc_final: 0.8256 (tp) outliers start: 25 outliers final: 17 residues processed: 73 average time/residue: 0.2549 time to fit residues: 25.8626 Evaluate side-chains 71 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 93 optimal weight: 30.0000 chunk 141 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10250 Z= 0.244 Angle : 0.604 11.049 14146 Z= 0.305 Chirality : 0.039 0.182 1677 Planarity : 0.004 0.046 1745 Dihedral : 16.920 95.013 2012 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.31 % Allowed : 19.70 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1359 helix: 2.66 (0.21), residues: 662 sheet: 0.28 (0.36), residues: 199 loop : -1.05 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 105 HIS 0.008 0.002 HIS B 284 PHE 0.015 0.001 PHE A 259 TYR 0.019 0.001 TYR B 131 ARG 0.008 0.001 ARG B 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 173 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7654 (mtm110) REVERT: B 39 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8664 (tt) REVERT: B 131 TYR cc_start: 0.8977 (t80) cc_final: 0.8630 (t80) REVERT: B 312 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8539 (tm-30) REVERT: F 90 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.6981 (m-80) REVERT: F 129 LEU cc_start: 0.8638 (mm) cc_final: 0.8178 (tp) outliers start: 17 outliers final: 13 residues processed: 73 average time/residue: 0.2584 time to fit residues: 25.8224 Evaluate side-chains 79 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 115 optimal weight: 0.0770 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.143510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099526 restraints weight = 54523.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.099395 restraints weight = 22196.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.100118 restraints weight = 14138.813| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10250 Z= 0.171 Angle : 0.557 10.717 14146 Z= 0.278 Chirality : 0.038 0.191 1677 Planarity : 0.004 0.048 1745 Dihedral : 16.598 92.790 2012 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.81 % Allowed : 20.20 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.24), residues: 1359 helix: 2.94 (0.21), residues: 665 sheet: 0.38 (0.36), residues: 206 loop : -0.87 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 105 HIS 0.008 0.001 HIS B 284 PHE 0.007 0.001 PHE A 259 TYR 0.016 0.001 TYR B 131 ARG 0.008 0.000 ARG B 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.31 seconds wall clock time: 33 minutes 51.18 seconds (2031.18 seconds total)