Starting phenix.real_space_refine (version: dev) on Sat Feb 18 17:08:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/02_2023/8e9y_27968_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/02_2023/8e9y_27968.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/02_2023/8e9y_27968_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/02_2023/8e9y_27968_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/02_2023/8e9y_27968_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/02_2023/8e9y_27968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/02_2023/8e9y_27968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/02_2023/8e9y_27968_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/02_2023/8e9y_27968_updated.pdb" } resolution = 2.79 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 Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 138": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8479 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2173 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1658 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2498 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} 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: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 385 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WE9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.35, per 1000 atoms: 0.63 Number of scatterers: 8479 At special positions: 0 Unit cell: (88, 118.8, 124.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 56 16.00 O 1562 8.00 N 1437 7.00 C 5423 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=2.04 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: 3.53 Conformation dependent library (CDL) restraints added in 1.5 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 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: 31 helices and 12 sheets defined 32.5% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 68 through 95 removed outlier: 3.750A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.571A pdb=" N LEU A 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 115 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 116 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 119 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 140 through 171 removed outlier: 4.122A pdb=" N TRP A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 145 " --> pdb=" O CYS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 No H-bonds generated for 'chain 'A' and resid 182 through 185' Processing helix chain 'A' and resid 187 through 205 removed outlier: 3.747A pdb=" N SER A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 207 through 210 No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.544A pdb=" N TYR A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 501 removed outlier: 3.879A pdb=" N ALA A 495 " --> pdb=" O GLN A 491 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 523 through 539 removed outlier: 4.205A pdb=" N TYR A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 535 " --> pdb=" O TRP A 531 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER A 537 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 538 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.565A pdb=" N THR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 29 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.682A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 146 through 155 removed outlier: 3.674A pdb=" N GLU B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.827A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 243 Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 34 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 9 through 24 Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.558A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 138 through 141 removed outlier: 3.966A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU B 36 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS B 82 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU B 38 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 79 through 83 removed outlier: 3.628A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.015A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.900A 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: 6.748A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 198 through 202 removed outlier: 3.817A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.485A 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: 6.661A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.395A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.738A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.727A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.613A 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: 6.233A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG E 168 " --> pdb=" O PRO E 173 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 147 344 hydrogen bonds defined for protein. 951 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: 2.49 Time building geometry restraints manager: 3.82 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: 2169 1.33 - 1.45: 1827 1.45 - 1.58: 4589 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8664 Sorted by residual: bond pdb=" N VAL B 186 " pdb=" CA VAL B 186 " ideal model delta sigma weight residual 1.461 1.502 -0.041 1.17e-02 7.31e+03 1.22e+01 bond pdb=" N VAL B 198 " pdb=" CA VAL B 198 " ideal model delta sigma weight residual 1.457 1.487 -0.030 9.30e-03 1.16e+04 1.04e+01 bond pdb=" N PRO B 184 " pdb=" CA PRO B 184 " ideal model delta sigma weight residual 1.474 1.450 0.024 7.40e-03 1.83e+04 1.02e+01 bond pdb=" N ASP B 183 " pdb=" CA ASP B 183 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.04e-02 9.25e+03 9.28e+00 bond pdb=" N ASP B 199 " pdb=" CA ASP B 199 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.27e-02 6.20e+03 8.88e+00 ... (remaining 8659 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.27: 134 105.27 - 112.46: 4489 112.46 - 119.65: 2782 119.65 - 126.84: 4284 126.84 - 134.03: 120 Bond angle restraints: 11809 Sorted by residual: angle pdb=" N TYR B 191 " pdb=" CA TYR B 191 " pdb=" C TYR B 191 " ideal model delta sigma weight residual 113.38 104.98 8.40 1.23e+00 6.61e-01 4.67e+01 angle pdb=" N ILE B 193 " pdb=" CA ILE B 193 " pdb=" C ILE B 193 " ideal model delta sigma weight residual 110.42 103.98 6.44 9.60e-01 1.09e+00 4.50e+01 angle pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " ideal model delta sigma weight residual 117.38 124.90 -7.52 1.18e+00 7.18e-01 4.06e+01 angle pdb=" N ILE B 200 " pdb=" CA ILE B 200 " pdb=" C ILE B 200 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.92e+01 angle pdb=" N VAL B 198 " pdb=" CA VAL B 198 " pdb=" C VAL B 198 " ideal model delta sigma weight residual 113.20 107.44 5.76 9.60e-01 1.09e+00 3.60e+01 ... (remaining 11804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4616 17.40 - 34.80: 371 34.80 - 52.20: 60 52.20 - 69.59: 10 69.59 - 86.99: 6 Dihedral angle restraints: 5063 sinusoidal: 1803 harmonic: 3260 Sorted by residual: dihedral pdb=" CA ASN D 24 " pdb=" C ASN D 24 " pdb=" N ILE D 25 " pdb=" CA ILE D 25 " ideal model delta harmonic sigma weight residual -180.00 -157.06 -22.94 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TYR E 161 " pdb=" C TYR E 161 " pdb=" N LEU E 162 " pdb=" CA LEU E 162 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 5060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1090 0.054 - 0.108: 243 0.108 - 0.162: 34 0.162 - 0.215: 4 0.215 - 0.269: 5 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CA ILE B 193 " pdb=" N ILE B 193 " pdb=" C ILE B 193 " pdb=" CB ILE B 193 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA GLU B 182 " pdb=" N GLU B 182 " pdb=" C GLU B 182 " pdb=" CB GLU B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE B 200 " pdb=" N ILE B 200 " pdb=" C ILE B 200 " pdb=" CB ILE B 200 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1373 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 212 " 0.063 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO B 213 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 193 " -0.018 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ILE B 193 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE B 193 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG B 194 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 222 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C GLU E 222 " 0.055 2.00e-02 2.50e+03 pdb=" O GLU E 222 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR E 223 " -0.019 2.00e-02 2.50e+03 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1193 2.75 - 3.29: 8493 3.29 - 3.83: 14170 3.83 - 4.36: 17096 4.36 - 4.90: 29115 Nonbonded interactions: 70067 Sorted by model distance: nonbonded pdb=" O SER B 44 " pdb=" ND2 ASN B 144 " model vdw 2.217 2.520 nonbonded pdb=" OG1 THR A 82 " pdb=" OG1 THR A 538 " model vdw 2.220 2.440 nonbonded pdb=" NH2 ARG A 177 " pdb=" OH TYR B 243 " model vdw 2.242 2.520 nonbonded pdb=" OH TYR C 264 " pdb=" O ALA C 299 " model vdw 2.243 2.440 nonbonded pdb=" O ALA B 41 " pdb=" OG SER B 44 " model vdw 2.244 2.440 ... (remaining 70062 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: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 1 4.86 5 C 5423 2.51 5 N 1437 2.21 5 O 1562 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: 2.430 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: 5.700 Check model and map are aligned: 0.120 Process input model: 26.610 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 8664 Z= 0.303 Angle : 0.810 13.182 11809 Z= 0.493 Chirality : 0.048 0.269 1376 Planarity : 0.004 0.096 1490 Dihedral : 13.306 86.992 2948 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1105 helix: -0.41 (0.26), residues: 374 sheet: -0.27 (0.32), residues: 259 loop : -1.06 (0.29), residues: 472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.010 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 172 average time/residue: 0.8271 time to fit residues: 155.6718 Evaluate side-chains 161 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.0030 chunk 33 optimal weight: 0.0980 chunk 51 optimal weight: 0.0060 chunk 63 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 overall best weight: 0.1606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8664 Z= 0.153 Angle : 0.570 7.208 11809 Z= 0.294 Chirality : 0.042 0.147 1376 Planarity : 0.004 0.065 1490 Dihedral : 5.930 98.101 1209 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.49 (0.26), residues: 1105 helix: 0.45 (0.27), residues: 372 sheet: -0.25 (0.31), residues: 267 loop : -0.91 (0.30), residues: 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 0.995 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 166 average time/residue: 0.9325 time to fit residues: 168.9178 Evaluate side-chains 160 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1332 time to fit residues: 1.9467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8664 Z= 0.229 Angle : 0.566 7.680 11809 Z= 0.293 Chirality : 0.042 0.132 1376 Planarity : 0.004 0.057 1490 Dihedral : 5.817 91.696 1209 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.37 (0.26), residues: 1105 helix: 0.67 (0.27), residues: 378 sheet: -0.15 (0.31), residues: 268 loop : -1.00 (0.30), residues: 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 0.962 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 163 average time/residue: 0.9025 time to fit residues: 159.9420 Evaluate side-chains 154 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.1575 time to fit residues: 2.2768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 99 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8664 Z= 0.170 Angle : 0.533 6.873 11809 Z= 0.273 Chirality : 0.041 0.129 1376 Planarity : 0.003 0.047 1490 Dihedral : 5.752 91.956 1209 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.27 (0.26), residues: 1105 helix: 0.79 (0.28), residues: 378 sheet: -0.13 (0.31), residues: 270 loop : -0.95 (0.30), residues: 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 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: 15 poor density : 160 time to evaluate : 0.917 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 167 average time/residue: 0.8399 time to fit residues: 153.4256 Evaluate side-chains 164 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.0833 time to fit residues: 1.6929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN C 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 8664 Z= 0.260 Angle : 0.579 7.488 11809 Z= 0.299 Chirality : 0.042 0.135 1376 Planarity : 0.004 0.046 1490 Dihedral : 5.828 90.048 1209 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.66 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.35 (0.26), residues: 1105 helix: 0.74 (0.27), residues: 381 sheet: -0.16 (0.31), residues: 270 loop : -1.04 (0.30), residues: 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 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: 21 poor density : 154 time to evaluate : 1.008 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 161 average time/residue: 0.8578 time to fit residues: 151.1139 Evaluate side-chains 159 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.5406 time to fit residues: 4.3688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 87 optimal weight: 0.0770 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 8664 Z= 0.258 Angle : 0.582 7.379 11809 Z= 0.300 Chirality : 0.042 0.130 1376 Planarity : 0.004 0.045 1490 Dihedral : 5.865 90.437 1209 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.37 (0.26), residues: 1105 helix: 0.71 (0.27), residues: 381 sheet: -0.17 (0.31), residues: 270 loop : -1.03 (0.30), residues: 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.051 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 164 average time/residue: 0.8569 time to fit residues: 153.7295 Evaluate side-chains 163 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 4 residues processed: 9 average time/residue: 0.2302 time to fit residues: 4.0780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 8664 Z= 0.276 Angle : 0.599 7.483 11809 Z= 0.309 Chirality : 0.043 0.137 1376 Planarity : 0.004 0.049 1490 Dihedral : 5.911 89.706 1209 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.44 (0.26), residues: 1105 helix: 0.65 (0.27), residues: 381 sheet: -0.21 (0.31), residues: 271 loop : -1.06 (0.30), residues: 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.028 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 163 average time/residue: 0.8722 time to fit residues: 156.1245 Evaluate side-chains 170 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 5 residues processed: 8 average time/residue: 0.1444 time to fit residues: 3.1035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.0670 chunk 9 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 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: 0.7501 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8664 Z= 0.169 Angle : 0.563 8.537 11809 Z= 0.289 Chirality : 0.041 0.128 1376 Planarity : 0.004 0.051 1490 Dihedral : 5.766 89.424 1209 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.33 (0.26), residues: 1105 helix: 0.72 (0.27), residues: 382 sheet: -0.15 (0.31), residues: 269 loop : -0.99 (0.30), residues: 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 0.859 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 167 average time/residue: 0.8385 time to fit residues: 153.6313 Evaluate side-chains 157 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1884 time to fit residues: 1.9335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN C 17 GLN E 82 GLN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8664 Z= 0.228 Angle : 0.583 7.600 11809 Z= 0.299 Chirality : 0.042 0.146 1376 Planarity : 0.004 0.052 1490 Dihedral : 5.757 87.886 1209 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.35 (0.26), residues: 1105 helix: 0.68 (0.27), residues: 380 sheet: -0.16 (0.31), residues: 269 loop : -0.98 (0.30), residues: 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.329 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 0.8653 time to fit residues: 151.5180 Evaluate side-chains 162 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 5 average time/residue: 0.1636 time to fit residues: 2.5551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.5980 chunk 71 optimal weight: 0.0870 chunk 108 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8664 Z= 0.205 Angle : 0.579 9.347 11809 Z= 0.298 Chirality : 0.042 0.145 1376 Planarity : 0.004 0.055 1490 Dihedral : 5.741 88.345 1209 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.31 (0.26), residues: 1105 helix: 0.68 (0.27), residues: 380 sheet: -0.10 (0.31), residues: 269 loop : -0.95 (0.30), residues: 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 0.905 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 159 average time/residue: 0.8876 time to fit residues: 154.0336 Evaluate side-chains 160 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1506 time to fit residues: 2.0687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.0980 chunk 12 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.161513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141823 restraints weight = 11794.634| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.79 r_work: 0.3753 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8664 Z= 0.173 Angle : 0.556 6.744 11809 Z= 0.284 Chirality : 0.041 0.141 1376 Planarity : 0.004 0.055 1490 Dihedral : 5.649 87.399 1209 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.07 % Favored : 95.84 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.24 (0.26), residues: 1105 helix: 0.73 (0.27), residues: 377 sheet: -0.09 (0.31), residues: 269 loop : -0.87 (0.30), residues: 459 =============================================================================== Job complete usr+sys time: 3281.56 seconds wall clock time: 59 minutes 33.95 seconds (3573.95 seconds total)