Starting phenix.real_space_refine (version: dev) on Sat Feb 18 17:53:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9w_27966/02_2023/8e9w_27966_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9w_27966/02_2023/8e9w_27966.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9w_27966/02_2023/8e9w_27966_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9w_27966/02_2023/8e9w_27966_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9w_27966/02_2023/8e9w_27966_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9w_27966/02_2023/8e9w_27966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9w_27966/02_2023/8e9w_27966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9w_27966/02_2023/8e9w_27966_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9w_27966/02_2023/8e9w_27966_updated.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8529 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2187 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1669 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 3 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2505 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 405 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1741 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'WEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.01, per 1000 atoms: 0.59 Number of scatterers: 8529 At special positions: 0 Unit cell: (116.16, 104.72, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1572 8.00 N 1450 7.00 C 5451 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.5 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 12 sheets defined 33.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 65 through 95 removed outlier: 5.436A pdb=" N PHE A 70 " --> pdb=" O TRP A 66 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 103 through 119 removed outlier: 3.874A pdb=" N PHE A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 119 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.656A pdb=" N ILE A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 171 removed outlier: 3.979A pdb=" N ASN A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 179 No H-bonds generated for 'chain 'A' and resid 176 through 179' Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.524A pdb=" N MET A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 241 through 264 Processing helix chain 'A' and resid 487 through 495 removed outlier: 3.858A pdb=" N GLN A 491 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 516 Proline residue: A 506 - end of helix removed outlier: 3.956A pdb=" N LEU A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 543 removed outlier: 3.978A pdb=" N TYR A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER A 537 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 538 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.532A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 184 through 203 removed outlier: 3.596A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.728A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 211 through 215 removed outlier: 7.409A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 36 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N HIS B 82 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU B 38 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.848A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.853A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.653A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.623A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.621A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.537A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.791A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 4 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.894A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.832A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 147 370 hydrogen bonds defined for protein. 1038 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: 2.48 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1621 1.33 - 1.45: 2253 1.45 - 1.57: 4760 1.57 - 1.69: 1 1.69 - 1.81: 78 Bond restraints: 8713 Sorted by residual: bond pdb=" C01 WEC A 601 " pdb=" N02 WEC A 601 " ideal model delta sigma weight residual 1.446 1.286 0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" C22 WEC A 601 " pdb=" N02 WEC A 601 " ideal model delta sigma weight residual 1.432 1.372 0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" C03 WEC A 601 " pdb=" N02 WEC A 601 " ideal model delta sigma weight residual 1.431 1.371 0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" N TYR B 170 " pdb=" CA TYR B 170 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.22e-02 6.72e+03 8.69e+00 bond pdb=" N THR E 226 " pdb=" CA THR E 226 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.27e-02 6.20e+03 7.99e+00 ... (remaining 8708 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.08: 201 107.08 - 113.86: 4920 113.86 - 120.63: 3510 120.63 - 127.41: 3144 127.41 - 134.18: 90 Bond angle restraints: 11865 Sorted by residual: angle pdb=" N PHE B 167 " pdb=" CA PHE B 167 " pdb=" C PHE B 167 " ideal model delta sigma weight residual 113.18 103.57 9.61 1.21e+00 6.83e-01 6.31e+01 angle pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " ideal model delta sigma weight residual 118.03 125.61 -7.58 1.19e+00 7.06e-01 4.06e+01 angle pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" O TYR E 223 " ideal model delta sigma weight residual 120.23 113.82 6.41 1.02e+00 9.61e-01 3.95e+01 angle pdb=" N PRO B 184 " pdb=" CA PRO B 184 " pdb=" C PRO B 184 " ideal model delta sigma weight residual 113.53 105.08 8.45 1.39e+00 5.18e-01 3.70e+01 angle pdb=" O PHE B 164 " pdb=" C PHE B 164 " pdb=" N PRO B 165 " ideal model delta sigma weight residual 120.83 114.42 6.41 1.06e+00 8.90e-01 3.66e+01 ... (remaining 11860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.24: 4735 19.24 - 38.48: 308 38.48 - 57.72: 41 57.72 - 76.96: 7 76.96 - 96.20: 5 Dihedral angle restraints: 5096 sinusoidal: 1836 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 520 " pdb=" CB CYS A 520 " ideal model delta sinusoidal sigma weight residual -86.00 -168.18 82.18 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 147.71 -54.71 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS A 141 " pdb=" SG CYS A 141 " pdb=" SG CYS A 221 " pdb=" CB CYS A 221 " ideal model delta sinusoidal sigma weight residual -86.00 -137.28 51.28 1 1.00e+01 1.00e-02 3.60e+01 ... (remaining 5093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1176 0.059 - 0.118: 190 0.118 - 0.177: 9 0.177 - 0.236: 2 0.236 - 0.295: 1 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA THR B 171 " pdb=" N THR B 171 " pdb=" C THR B 171 " pdb=" CB THR B 171 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA TYR E 223 " pdb=" N TYR E 223 " pdb=" C TYR E 223 " pdb=" CB TYR E 223 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ARG B 169 " pdb=" N ARG B 169 " pdb=" C ARG B 169 " pdb=" CB ARG B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 1375 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 171 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C THR B 171 " -0.062 2.00e-02 2.50e+03 pdb=" O THR B 171 " 0.023 2.00e-02 2.50e+03 pdb=" N THR B 172 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 183 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C LYS A 183 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS A 183 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 184 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 54 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO D 55 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 55 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 55 " -0.023 5.00e-02 4.00e+02 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 883 2.75 - 3.29: 8347 3.29 - 3.82: 14164 3.82 - 4.36: 17002 4.36 - 4.90: 29640 Nonbonded interactions: 70036 Sorted by model distance: nonbonded pdb=" O LEU A 512 " pdb=" OG1 THR A 515 " model vdw 2.210 2.440 nonbonded pdb=" OG1 THR A 82 " pdb=" OG1 THR A 538 " model vdw 2.214 2.440 nonbonded pdb=" O LEU A 88 " pdb=" OG SER A 92 " model vdw 2.230 2.440 nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.234 2.440 nonbonded pdb=" NH1 ARG C 49 " pdb=" O TYR C 85 " model vdw 2.243 2.520 ... (remaining 70031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5451 2.51 5 N 1450 2.21 5 O 1572 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.590 Check model and map are aligned: 0.120 Process input model: 25.450 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 0.160 8713 Z= 0.226 Angle : 0.673 13.437 11865 Z= 0.382 Chirality : 0.043 0.295 1378 Planarity : 0.003 0.041 1497 Dihedral : 12.895 96.196 2981 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.11 % 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: 0.23 (0.26), residues: 1103 helix: 0.42 (0.27), residues: 377 sheet: 0.92 (0.32), residues: 285 loop : -0.49 (0.30), residues: 441 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.021 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.9365 time to fit residues: 170.5076 Evaluate side-chains 155 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.0270 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN C 75 GLN C 125 ASN C 266 HIS E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8713 Z= 0.209 Angle : 0.527 6.890 11865 Z= 0.278 Chirality : 0.042 0.142 1378 Planarity : 0.004 0.041 1497 Dihedral : 6.019 106.985 1216 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.91 % 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: 0.59 (0.26), residues: 1103 helix: 0.95 (0.28), residues: 399 sheet: 0.73 (0.31), residues: 291 loop : -0.29 (0.31), residues: 413 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 1.009 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 181 average time/residue: 1.1870 time to fit residues: 230.1255 Evaluate side-chains 178 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.1846 time to fit residues: 1.8866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN B 244 ASN C 125 ASN C 132 ASN C 266 HIS E 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 8713 Z= 0.233 Angle : 0.529 9.929 11865 Z= 0.276 Chirality : 0.043 0.139 1378 Planarity : 0.003 0.040 1497 Dihedral : 6.041 106.447 1216 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.48 % 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: 0.51 (0.26), residues: 1103 helix: 0.96 (0.28), residues: 400 sheet: 0.44 (0.29), residues: 308 loop : -0.24 (0.32), residues: 395 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 1.061 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 179 average time/residue: 1.2397 time to fit residues: 236.3507 Evaluate side-chains 180 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 2 residues processed: 8 average time/residue: 0.7966 time to fit residues: 8.2529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN C 125 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8713 Z= 0.218 Angle : 0.513 10.550 11865 Z= 0.267 Chirality : 0.042 0.139 1378 Planarity : 0.003 0.040 1497 Dihedral : 6.031 106.904 1216 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 2.17 % 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: 0.58 (0.26), residues: 1103 helix: 1.04 (0.28), residues: 399 sheet: 0.55 (0.30), residues: 291 loop : -0.25 (0.31), residues: 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 0.932 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 175 average time/residue: 1.1970 time to fit residues: 223.1230 Evaluate side-chains 186 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 3 residues processed: 10 average time/residue: 0.5303 time to fit residues: 7.2261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8713 Z= 0.276 Angle : 0.547 12.535 11865 Z= 0.282 Chirality : 0.043 0.197 1378 Planarity : 0.003 0.041 1497 Dihedral : 6.103 106.789 1216 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 2.74 % 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: 0.50 (0.26), residues: 1103 helix: 0.99 (0.28), residues: 399 sheet: 0.50 (0.30), residues: 282 loop : -0.30 (0.30), residues: 422 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 0.993 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 188 average time/residue: 1.1571 time to fit residues: 232.2732 Evaluate side-chains 182 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 4 residues processed: 10 average time/residue: 0.7798 time to fit residues: 9.7322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN C 125 ASN E 82 GLN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8713 Z= 0.200 Angle : 0.518 11.483 11865 Z= 0.269 Chirality : 0.042 0.140 1378 Planarity : 0.003 0.042 1497 Dihedral : 6.011 106.930 1216 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 2.62 % 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: 0.57 (0.26), residues: 1103 helix: 1.08 (0.28), residues: 399 sheet: 0.48 (0.30), residues: 285 loop : -0.25 (0.31), residues: 419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 0.959 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 182 average time/residue: 1.1882 time to fit residues: 230.6372 Evaluate side-chains 180 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 5 residues processed: 9 average time/residue: 0.6146 time to fit residues: 7.4989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN C 110 ASN C 125 ASN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 8713 Z= 0.263 Angle : 0.558 12.745 11865 Z= 0.287 Chirality : 0.044 0.187 1378 Planarity : 0.004 0.041 1497 Dihedral : 6.097 106.910 1216 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 2.39 % 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: 0.53 (0.26), residues: 1103 helix: 1.09 (0.27), residues: 393 sheet: 0.44 (0.30), residues: 287 loop : -0.29 (0.30), residues: 423 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 0.982 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 170 average time/residue: 1.2119 time to fit residues: 220.1158 Evaluate side-chains 171 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 0.4172 time to fit residues: 4.7630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8713 Z= 0.238 Angle : 0.548 12.256 11865 Z= 0.282 Chirality : 0.043 0.147 1378 Planarity : 0.004 0.040 1497 Dihedral : 6.067 106.858 1216 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.39 % 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: 0.57 (0.26), residues: 1103 helix: 1.14 (0.28), residues: 393 sheet: 0.46 (0.30), residues: 285 loop : -0.27 (0.30), residues: 425 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 0.966 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 170 average time/residue: 1.2298 time to fit residues: 223.0060 Evaluate side-chains 172 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 5 average time/residue: 0.1954 time to fit residues: 2.7769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.0170 chunk 63 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 8713 Z= 0.230 Angle : 0.547 12.131 11865 Z= 0.283 Chirality : 0.043 0.139 1378 Planarity : 0.004 0.041 1497 Dihedral : 6.065 106.913 1216 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 1.94 % 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: 0.60 (0.26), residues: 1103 helix: 1.17 (0.28), residues: 392 sheet: 0.40 (0.30), residues: 291 loop : -0.20 (0.30), residues: 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 0.807 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 170 average time/residue: 1.1556 time to fit residues: 209.9542 Evaluate side-chains 171 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 6 average time/residue: 0.4750 time to fit residues: 4.5532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 53 optimal weight: 0.4980 chunk 69 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8713 Z= 0.194 Angle : 0.530 10.809 11865 Z= 0.274 Chirality : 0.042 0.150 1378 Planarity : 0.004 0.048 1497 Dihedral : 6.000 107.066 1216 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.60 % 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: 0.64 (0.26), residues: 1103 helix: 1.23 (0.28), residues: 392 sheet: 0.40 (0.30), residues: 291 loop : -0.19 (0.31), residues: 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 1.031 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 173 average time/residue: 1.1549 time to fit residues: 213.6641 Evaluate side-chains 170 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 0.1685 time to fit residues: 1.8340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 0.0000 chunk 16 optimal weight: 0.0870 chunk 76 optimal weight: 0.0370 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 overall best weight: 0.3240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 110 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.134814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116394 restraints weight = 11679.325| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.79 r_work: 0.3413 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8713 Z= 0.155 Angle : 0.504 8.247 11865 Z= 0.264 Chirality : 0.041 0.140 1378 Planarity : 0.003 0.044 1497 Dihedral : 5.884 107.319 1216 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 1.71 % 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: 0.74 (0.26), residues: 1103 helix: 1.34 (0.28), residues: 392 sheet: 0.47 (0.30), residues: 290 loop : -0.17 (0.31), residues: 421 =============================================================================== Job complete usr+sys time: 3935.97 seconds wall clock time: 70 minutes 31.35 seconds (4231.35 seconds total)