Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 18:31:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxr_21962/04_2023/6wxr_21962_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxr_21962/04_2023/6wxr_21962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxr_21962/04_2023/6wxr_21962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxr_21962/04_2023/6wxr_21962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxr_21962/04_2023/6wxr_21962_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxr_21962/04_2023/6wxr_21962_updated.pdb" } resolution = 3.2 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= 0.011 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 S 42 5.16 5 C 6775 2.51 5 N 1776 2.21 5 O 1812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A ARG 618": "NH1" <-> "NH2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A GLU 1114": "OE1" <-> "OE2" Residue "A ARG 1215": "NH1" <-> "NH2" Residue "A ARG 1216": "NH1" <-> "NH2" Residue "A ARG 1248": "NH1" <-> "NH2" Residue "A ARG 1270": "NH1" <-> "NH2" Residue "A ARG 1291": "NH1" <-> "NH2" Residue "A ARG 1345": "NH1" <-> "NH2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1437": "NH1" <-> "NH2" Residue "A ARG 1538": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10409 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8409 Classifications: {'peptide': 1075} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 70, 'TRANS': 1004} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 12, 'ASN:plan1': 4, 'HIS:plan': 3, 'GLU:plan': 17, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 194 Chain: "B" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1744 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 216} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 181 Unusual residues: {'FAD': 1, 'HEM': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.96, per 1000 atoms: 0.57 Number of scatterers: 10409 At special positions: 0 Unit cell: (89.64, 99.36, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 42 16.00 P 2 15.00 O 1812 8.00 N 1776 7.00 C 6775 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A1165 " distance=2.04 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 234 " 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 Links applied ALPHA1-3 " MAN C 4 " - " MAN C 5 " ALPHA1-6 " BMA C 3 " - " MAN C 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A1602 " - " ASN A 94 " " NAG A1603 " - " ASN A 342 " " NAG A1604 " - " ASN A 534 " " NAG B 406 " - " ASN B 84 " " NAG C 1 " - " ASN B 109 " Time building additional restraints: 4.47 Conformation dependent library (CDL) restraints added in 1.5 seconds 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 5 sheets defined 42.1% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 75 through 82 removed outlier: 3.671A pdb=" N ASN A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.689A pdb=" N SER A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 removed outlier: 4.075A pdb=" N LEU A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 299 Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 320 through 332 removed outlier: 4.813A pdb=" N THR A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 removed outlier: 4.028A pdb=" N SER A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 405 No H-bonds generated for 'chain 'A' and resid 402 through 405' Processing helix chain 'A' and resid 420 through 429 removed outlier: 3.584A pdb=" N LEU A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.521A pdb=" N LEU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 495 through 510 removed outlier: 3.818A pdb=" N THR A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 534 removed outlier: 4.102A pdb=" N ASN A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 545 Processing helix chain 'A' and resid 593 through 620 removed outlier: 3.604A pdb=" N PHE A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 1030 through 1040 Processing helix chain 'A' and resid 1042 through 1067 Processing helix chain 'A' and resid 1080 through 1103 removed outlier: 4.295A pdb=" N ALA A1091 " --> pdb=" O ARG A1087 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A1092 " --> pdb=" O GLY A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1114 removed outlier: 4.424A pdb=" N GLU A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1155 Processing helix chain 'A' and resid 1160 through 1166 removed outlier: 4.448A pdb=" N CYS A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1187 Processing helix chain 'A' and resid 1190 through 1207 Processing helix chain 'A' and resid 1211 through 1214 No H-bonds generated for 'chain 'A' and resid 1211 through 1214' Processing helix chain 'A' and resid 1218 through 1239 removed outlier: 3.514A pdb=" N HIS A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N HIS A1226 " --> pdb=" O TRP A1222 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU A1227 " --> pdb=" O LEU A1223 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TYR A1228 " --> pdb=" O THR A1224 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE A1229 " --> pdb=" O HIS A1225 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A1230 " --> pdb=" O HIS A1226 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A1236 " --> pdb=" O TYR A1232 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A1239 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1269 removed outlier: 3.838A pdb=" N LEU A1254 " --> pdb=" O HIS A1250 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A1255 " --> pdb=" O ILE A1251 " (cutoff:3.500A) Proline residue: A1256 - end of helix Processing helix chain 'A' and resid 1284 through 1286 No H-bonds generated for 'chain 'A' and resid 1284 through 1286' Processing helix chain 'A' and resid 1341 through 1349 Processing helix chain 'A' and resid 1376 through 1378 No H-bonds generated for 'chain 'A' and resid 1376 through 1378' Processing helix chain 'A' and resid 1389 through 1392 removed outlier: 3.736A pdb=" N VAL A1392 " --> pdb=" O GLY A1389 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1389 through 1392' Processing helix chain 'A' and resid 1395 through 1409 Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1498 through 1508 removed outlier: 3.938A pdb=" N PHE A1502 " --> pdb=" O PHE A1498 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN A1503 " --> pdb=" O GLU A1499 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1507 " --> pdb=" O ASN A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1537 Processing helix chain 'B' and resid 51 through 72 Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'B' and resid 152 through 161 removed outlier: 4.075A pdb=" N PHE B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 3.828A pdb=" N HIS B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 4.066A pdb=" N TRP B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 206 No H-bonds generated for 'chain 'B' and resid 203 through 206' Processing helix chain 'B' and resid 209 through 218 removed outlier: 3.780A pdb=" N GLY B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 249 through 274 Processing sheet with id= A, first strand: chain 'A' and resid 1288 through 1291 removed outlier: 3.665A pdb=" N ILE A1336 " --> pdb=" O THR A1288 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1305 through 1308 Processing sheet with id= C, first strand: chain 'A' and resid 1384 through 1388 removed outlier: 6.361A pdb=" N TYR A1418 " --> pdb=" O LEU A1385 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLY A1387 " --> pdb=" O TYR A1418 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A1420 " --> pdb=" O GLY A1387 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER A1449 " --> pdb=" O PHE A1419 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TRP A1421 " --> pdb=" O SER A1449 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS A1451 " --> pdb=" O TRP A1421 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 77 through 79 Processing sheet with id= E, first strand: chain 'B' and resid 81 through 86 360 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1556 1.30 - 1.44: 3285 1.44 - 1.59: 5823 1.59 - 1.73: 3 1.73 - 1.87: 71 Bond restraints: 10738 Sorted by residual: bond pdb=" C3B HEM A1605 " pdb=" C4B HEM A1605 " ideal model delta sigma weight residual 1.449 1.292 0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" C ILE A1237 " pdb=" O ILE A1237 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.23e-02 6.61e+03 4.11e+01 bond pdb=" CAB HEM A1605 " pdb=" CBB HEM A1605 " ideal model delta sigma weight residual 1.337 1.209 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C3B HEM A1606 " pdb=" C4B HEM A1606 " ideal model delta sigma weight residual 1.449 1.323 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C HIS A1238 " pdb=" O HIS A1238 " ideal model delta sigma weight residual 1.237 1.163 0.073 1.17e-02 7.31e+03 3.93e+01 ... (remaining 10733 not shown) Histogram of bond angle deviations from ideal: 89.51 - 107.58: 601 107.58 - 125.65: 13764 125.65 - 143.72: 309 143.72 - 161.79: 0 161.79 - 179.87: 4 Bond angle restraints: 14678 Sorted by residual: angle pdb=" N PRO A1352 " pdb=" CA PRO A1352 " pdb=" CB PRO A1352 " ideal model delta sigma weight residual 103.08 110.67 -7.59 9.70e-01 1.06e+00 6.12e+01 angle pdb=" C1C HEM A1605 " pdb=" CHC HEM A1605 " pdb=" C4B HEM A1605 " ideal model delta sigma weight residual 126.00 112.17 13.83 3.00e+00 1.11e-01 2.12e+01 angle pdb=" C SER A1240 " pdb=" N PHE A1241 " pdb=" CA PHE A1241 " ideal model delta sigma weight residual 121.91 130.78 -8.87 2.03e+00 2.43e-01 1.91e+01 angle pdb=" CA ILE A1237 " pdb=" C ILE A1237 " pdb=" N HIS A1238 " ideal model delta sigma weight residual 117.53 122.67 -5.14 1.19e+00 7.06e-01 1.87e+01 angle pdb=" C LEU A1235 " pdb=" N ILE A1236 " pdb=" CA ILE A1236 " ideal model delta sigma weight residual 122.35 117.31 5.04 1.18e+00 7.18e-01 1.82e+01 ... (remaining 14673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5457 17.98 - 35.96: 521 35.96 - 53.94: 81 53.94 - 71.93: 13 71.93 - 89.91: 7 Dihedral angle restraints: 6079 sinusoidal: 2322 harmonic: 3757 Sorted by residual: dihedral pdb=" CA CYS A 118 " pdb=" C CYS A 118 " pdb=" N PRO A 119 " pdb=" CA PRO A 119 " ideal model delta harmonic sigma weight residual 180.00 116.55 63.45 0 5.00e+00 4.00e-02 1.61e+02 dihedral pdb=" CA THR B 115 " pdb=" C THR B 115 " pdb=" N PRO B 116 " pdb=" CA PRO B 116 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" C2C HEM A1606 " pdb=" C3C HEM A1606 " pdb=" CAC HEM A1606 " pdb=" CBC HEM A1606 " ideal model delta sinusoidal sigma weight residual 180.00 132.40 47.60 2 1.00e+01 1.00e-02 2.62e+01 ... (remaining 6076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1480 0.074 - 0.147: 134 0.147 - 0.221: 3 0.221 - 0.295: 2 0.295 - 0.368: 1 Chirality restraints: 1620 Sorted by residual: chirality pdb=" C1 NAG A1604 " pdb=" ND2 ASN A 534 " pdb=" C2 NAG A1604 " pdb=" O5 NAG A1604 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PRO A1352 " pdb=" N PRO A1352 " pdb=" C PRO A1352 " pdb=" CB PRO A1352 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1617 not shown) Planarity restraints: 1837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1235 " -0.026 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C LEU A1235 " 0.088 2.00e-02 2.50e+03 pdb=" O LEU A1235 " -0.032 2.00e-02 2.50e+03 pdb=" N ILE A1236 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEM A1605 " -0.001 2.00e-02 2.50e+03 2.66e-02 1.59e+01 pdb=" C1D HEM A1605 " 0.007 2.00e-02 2.50e+03 pdb=" C2D HEM A1605 " 0.013 2.00e-02 2.50e+03 pdb=" C3D HEM A1605 " -0.061 2.00e-02 2.50e+03 pdb=" C4D HEM A1605 " 0.010 2.00e-02 2.50e+03 pdb=" CAD HEM A1605 " -0.007 2.00e-02 2.50e+03 pdb=" CHA HEM A1605 " 0.025 2.00e-02 2.50e+03 pdb=" CHD HEM A1605 " -0.021 2.00e-02 2.50e+03 pdb=" CMD HEM A1605 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM A1605 " -0.060 2.00e-02 2.50e+03 2.52e-02 1.43e+01 pdb=" C2A HEM A1605 " 0.003 2.00e-02 2.50e+03 pdb=" C3A HEM A1605 " -0.004 2.00e-02 2.50e+03 pdb=" C4A HEM A1605 " 0.031 2.00e-02 2.50e+03 pdb=" CAA HEM A1605 " 0.000 2.00e-02 2.50e+03 pdb=" CHA HEM A1605 " 0.027 2.00e-02 2.50e+03 pdb=" CHB HEM A1605 " -0.016 2.00e-02 2.50e+03 pdb=" CMA HEM A1605 " 0.006 2.00e-02 2.50e+03 pdb=" NA HEM A1605 " 0.013 2.00e-02 2.50e+03 ... (remaining 1834 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 5 2.19 - 2.87: 3834 2.87 - 3.55: 14123 3.55 - 4.22: 23433 4.22 - 4.90: 41666 Nonbonded interactions: 83061 Sorted by model distance: nonbonded pdb=" CE1 HIS A1238 " pdb="FE HEM A1606 " model vdw 1.518 3.220 nonbonded pdb=" O2' FAD A1601 " pdb=" O4' FAD A1601 " model vdw 1.995 2.440 nonbonded pdb=" CE1 HIS A1238 " pdb=" NA HEM A1606 " model vdw 2.027 3.340 nonbonded pdb=" O SER A1240 " pdb=" OG SER A1240 " model vdw 2.040 2.440 nonbonded pdb=" OH TYR A 36 " pdb=" O LEU B 146 " model vdw 2.137 2.440 ... (remaining 83056 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 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: 0.550 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: 3.410 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.890 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 0.011 0.263 10738 Z= 0.675 Angle : 0.963 13.825 14678 Z= 0.484 Chirality : 0.044 0.368 1620 Planarity : 0.005 0.055 1832 Dihedral : 14.151 89.908 3655 Min Nonbonded Distance : 1.518 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.61 % Favored : 93.31 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -3.63 (0.20), residues: 1285 helix: -1.77 (0.18), residues: 613 sheet: -1.86 (0.47), residues: 110 loop : -3.25 (0.22), residues: 562 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.184 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 110 average time/residue: 0.3027 time to fit residues: 45.4280 Evaluate side-chains 79 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1007 time to fit residues: 1.9872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.0270 chunk 117 optimal weight: 1.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 504 GLN A1107 ASN A1212 HIS A1238 HIS A1319 HIS B 71 ASN B 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 10738 Z= 0.184 Angle : 0.680 12.315 14678 Z= 0.309 Chirality : 0.044 0.428 1620 Planarity : 0.005 0.059 1832 Dihedral : 7.165 87.874 1439 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -2.35 (0.22), residues: 1285 helix: -0.57 (0.20), residues: 597 sheet: -1.63 (0.46), residues: 118 loop : -2.64 (0.25), residues: 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 1.228 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 97 average time/residue: 0.2449 time to fit residues: 34.2243 Evaluate side-chains 88 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1047 time to fit residues: 3.3929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 0.0060 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 94 optimal weight: 5.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A1130 HIS B 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10738 Z= 0.181 Angle : 0.643 11.971 14678 Z= 0.296 Chirality : 0.044 0.431 1620 Planarity : 0.004 0.057 1832 Dihedral : 7.113 81.710 1439 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.09 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.69 (0.23), residues: 1285 helix: 0.06 (0.21), residues: 588 sheet: -1.32 (0.48), residues: 118 loop : -2.37 (0.25), residues: 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 1.156 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 97 average time/residue: 0.2340 time to fit residues: 33.0456 Evaluate side-chains 82 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1054 time to fit residues: 2.4709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1226 HIS B 178 HIS B 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 10738 Z= 0.361 Angle : 0.737 11.844 14678 Z= 0.347 Chirality : 0.048 0.414 1620 Planarity : 0.005 0.058 1832 Dihedral : 7.383 84.928 1439 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.16 % Favored : 92.76 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.68 (0.23), residues: 1285 helix: 0.09 (0.21), residues: 590 sheet: -1.37 (0.48), residues: 118 loop : -2.38 (0.25), residues: 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.202 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 94 average time/residue: 0.2511 time to fit residues: 34.2517 Evaluate side-chains 87 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0984 time to fit residues: 3.2130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN B 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 10738 Z= 0.228 Angle : 0.659 12.206 14678 Z= 0.309 Chirality : 0.045 0.423 1620 Planarity : 0.005 0.055 1832 Dihedral : 7.256 85.913 1439 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.23), residues: 1285 helix: 0.27 (0.22), residues: 594 sheet: -1.34 (0.48), residues: 118 loop : -2.21 (0.25), residues: 573 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 1.173 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 101 average time/residue: 0.3128 time to fit residues: 45.1721 Evaluate side-chains 89 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1193 time to fit residues: 2.6290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1225 HIS A1375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 10738 Z= 0.338 Angle : 0.721 12.050 14678 Z= 0.340 Chirality : 0.047 0.406 1620 Planarity : 0.005 0.057 1832 Dihedral : 7.415 86.983 1439 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.94 % Favored : 91.98 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.50 (0.23), residues: 1285 helix: 0.21 (0.21), residues: 595 sheet: -1.48 (0.46), residues: 120 loop : -2.22 (0.25), residues: 570 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.289 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 94 average time/residue: 0.2516 time to fit residues: 34.0790 Evaluate side-chains 86 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1047 time to fit residues: 3.0164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 10738 Z= 0.310 Angle : 0.714 12.262 14678 Z= 0.333 Chirality : 0.047 0.406 1620 Planarity : 0.005 0.054 1832 Dihedral : 7.361 88.835 1439 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.63 % Favored : 92.30 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.23), residues: 1285 helix: 0.24 (0.21), residues: 595 sheet: -1.41 (0.47), residues: 120 loop : -2.18 (0.26), residues: 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 1.185 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 91 average time/residue: 0.2535 time to fit residues: 33.5668 Evaluate side-chains 84 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1066 time to fit residues: 2.5855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 0.0030 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 10738 Z= 0.185 Angle : 0.650 12.243 14678 Z= 0.300 Chirality : 0.044 0.420 1620 Planarity : 0.004 0.055 1832 Dihedral : 7.180 88.358 1439 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.23 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.17 (0.24), residues: 1285 helix: 0.54 (0.22), residues: 589 sheet: -1.34 (0.48), residues: 118 loop : -2.09 (0.25), residues: 578 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.093 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 92 average time/residue: 0.2460 time to fit residues: 32.7381 Evaluate side-chains 83 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1034 time to fit residues: 2.0204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 0.0000 chunk 109 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 10738 Z= 0.206 Angle : 0.664 12.066 14678 Z= 0.306 Chirality : 0.044 0.413 1620 Planarity : 0.005 0.054 1832 Dihedral : 7.127 88.959 1439 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.61 % Favored : 93.31 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.12 (0.24), residues: 1285 helix: 0.57 (0.22), residues: 592 sheet: -1.32 (0.47), residues: 118 loop : -2.06 (0.25), residues: 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 1.197 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 88 average time/residue: 0.2554 time to fit residues: 32.2996 Evaluate side-chains 87 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1017 time to fit residues: 1.8321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 10738 Z= 0.199 Angle : 0.653 12.153 14678 Z= 0.302 Chirality : 0.044 0.416 1620 Planarity : 0.005 0.055 1832 Dihedral : 6.954 89.558 1439 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.39 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.02 (0.24), residues: 1285 helix: 0.67 (0.22), residues: 589 sheet: -1.27 (0.48), residues: 118 loop : -2.02 (0.25), residues: 578 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.320 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 89 average time/residue: 0.2458 time to fit residues: 31.7702 Evaluate side-chains 88 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1121 time to fit residues: 2.3225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 105 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.157251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.122552 restraints weight = 16355.176| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.20 r_work: 0.3582 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 10738 Z= 0.218 Angle : 0.663 12.137 14678 Z= 0.305 Chirality : 0.044 0.412 1620 Planarity : 0.005 0.054 1832 Dihedral : 6.635 89.971 1439 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.93 % Favored : 93.00 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -1.00 (0.24), residues: 1285 helix: 0.70 (0.22), residues: 589 sheet: -1.29 (0.48), residues: 118 loop : -2.02 (0.25), residues: 578 =============================================================================== Job complete usr+sys time: 2029.59 seconds wall clock time: 37 minutes 56.29 seconds (2276.29 seconds total)