Starting phenix.real_space_refine on Fri Mar 15 02:31:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxr_21962/03_2024/6wxr_21962_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxr_21962/03_2024/6wxr_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_21962/03_2024/6wxr_21962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxr_21962/03_2024/6wxr_21962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxr_21962/03_2024/6wxr_21962_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxr_21962/03_2024/6wxr_21962_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.37, per 1000 atoms: 0.61 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: 4.31 Conformation dependent library (CDL) restraints added in 1.9 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: 2.66 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: 2.62 Time building geometry restraints manager: 4.68 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 - 22.68: 5837 22.68 - 45.36: 399 45.36 - 68.04: 51 68.04 - 90.72: 11 90.72 - 113.39: 7 Dihedral angle restraints: 6305 sinusoidal: 2548 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 6302 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: 0.490 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: 3.150 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 31.660 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- 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 : 15.608 113.394 3881 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 % Allowed : 4.96 % Favored : 94.85 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1421 HIS 0.014 0.001 HIS A1238 PHE 0.014 0.001 PHE B 222 TYR 0.014 0.001 TYR A1099 ARG 0.003 0.000 ARG A 76 *********************** 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 : 1.226 Fit side-chains revert: symmetry clash REVERT: A 1495 ARG cc_start: 0.7145 (mmm160) cc_final: 0.6819 (ptp90) REVERT: A 1501 PHE cc_start: 0.7263 (t80) cc_final: 0.6877 (t80) REVERT: B 136 ARG cc_start: 0.7698 (mtp85) cc_final: 0.7304 (mtp180) REVERT: B 197 MET cc_start: 0.7935 (mtt) cc_final: 0.7693 (mtt) outliers start: 2 outliers final: 2 residues processed: 110 average time/residue: 0.2849 time to fit residues: 42.8819 Evaluate side-chains 79 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1240 SER 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: 0.6980 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: 9.9990 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: 0.5238 ------------------------------------------------------------------------------- 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: 0.7690 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 10738 Z= 0.178 Angle : 0.678 12.104 14678 Z= 0.306 Chirality : 0.042 0.289 1620 Planarity : 0.005 0.060 1832 Dihedral : 10.863 88.311 1668 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.61 % Favored : 93.31 % Rotamer: Outliers : 1.24 % Allowed : 8.39 % Favored : 90.37 % 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: -2.28 (0.22), residues: 1285 helix: -0.50 (0.20), residues: 597 sheet: -1.62 (0.46), residues: 118 loop : -2.62 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 614 HIS 0.004 0.001 HIS A1144 PHE 0.014 0.001 PHE A 253 TYR 0.013 0.001 TYR A1099 ARG 0.003 0.000 ARG A1424 *********************** 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 103 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.284 Fit side-chains REVERT: A 265 GLN cc_start: 0.7294 (mp10) cc_final: 0.7019 (mp10) REVERT: A 300 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7979 (pp) REVERT: A 1241 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: A 1288 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8682 (t) REVERT: A 1495 ARG cc_start: 0.7057 (mmm160) cc_final: 0.6778 (ptp90) REVERT: A 1501 PHE cc_start: 0.7201 (t80) cc_final: 0.6868 (t80) REVERT: B 136 ARG cc_start: 0.7670 (mtp85) cc_final: 0.7259 (mtp180) outliers start: 13 outliers final: 6 residues processed: 99 average time/residue: 0.2446 time to fit residues: 34.1882 Evaluate side-chains 86 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 242 VAL 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: 0.0000 chunk 79 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 0.0270 chunk 104 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.7444 ------------------------------------------------------------------------------- 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: 0.7684 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10738 Z= 0.169 Angle : 0.626 11.974 14678 Z= 0.289 Chirality : 0.041 0.293 1620 Planarity : 0.004 0.058 1832 Dihedral : 10.243 82.473 1665 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 1.72 % Allowed : 9.72 % Favored : 88.56 % 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: -1.59 (0.23), residues: 1285 helix: 0.14 (0.21), residues: 590 sheet: -1.35 (0.48), residues: 118 loop : -2.30 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1421 HIS 0.004 0.001 HIS A1144 PHE 0.022 0.001 PHE A1404 TYR 0.010 0.001 TYR A1099 ARG 0.003 0.000 ARG A1424 *********************** 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 104 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 1.195 Fit side-chains REVERT: A 265 GLN cc_start: 0.7340 (mp10) cc_final: 0.7136 (mp10) REVERT: A 300 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7988 (pp) REVERT: A 1241 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: A 1288 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8640 (t) REVERT: A 1495 ARG cc_start: 0.7043 (mmm160) cc_final: 0.6784 (ptp90) REVERT: A 1501 PHE cc_start: 0.7218 (t80) cc_final: 0.6896 (t80) REVERT: B 136 ARG cc_start: 0.7693 (mtp85) cc_final: 0.7272 (mtp180) REVERT: B 179 TYR cc_start: 0.7862 (m-10) cc_final: 0.7597 (m-80) outliers start: 18 outliers final: 8 residues processed: 100 average time/residue: 0.2413 time to fit residues: 34.6073 Evaluate side-chains 88 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.1562 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= 0.172 Angle : 0.606 11.538 14678 Z= 0.285 Chirality : 0.042 0.294 1620 Planarity : 0.004 0.059 1832 Dihedral : 9.900 81.956 1665 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 1.91 % Allowed : 11.06 % Favored : 87.04 % 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: -1.28 (0.23), residues: 1285 helix: 0.42 (0.22), residues: 589 sheet: -1.31 (0.48), residues: 118 loop : -2.14 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1421 HIS 0.004 0.001 HIS A1144 PHE 0.013 0.001 PHE A 253 TYR 0.011 0.001 TYR B 170 ARG 0.003 0.000 ARG A1424 *********************** 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 103 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.179 Fit side-chains REVERT: A 300 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8059 (pp) REVERT: A 1241 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7135 (m-80) REVERT: A 1288 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8654 (t) REVERT: A 1495 ARG cc_start: 0.7036 (mmm160) cc_final: 0.6766 (ptp90) REVERT: A 1501 PHE cc_start: 0.7215 (t80) cc_final: 0.6909 (t80) REVERT: B 136 ARG cc_start: 0.7671 (mtp85) cc_final: 0.7247 (mtp180) outliers start: 20 outliers final: 8 residues processed: 96 average time/residue: 0.2251 time to fit residues: 31.4399 Evaluate side-chains 92 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10738 Z= 0.299 Angle : 0.681 11.821 14678 Z= 0.322 Chirality : 0.045 0.304 1620 Planarity : 0.005 0.059 1832 Dihedral : 9.751 83.651 1665 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.84 % Rotamer: Outliers : 2.38 % Allowed : 12.58 % Favored : 85.03 % 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: -1.37 (0.23), residues: 1285 helix: 0.31 (0.21), residues: 596 sheet: -1.27 (0.48), residues: 118 loop : -2.17 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1421 HIS 0.006 0.001 HIS A1225 PHE 0.025 0.002 PHE A1370 TYR 0.013 0.002 TYR A1099 ARG 0.005 0.000 ARG A 509 *********************** 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 106 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 1.246 Fit side-chains REVERT: A 300 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8081 (pp) REVERT: A 1241 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: A 1288 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8684 (t) REVERT: A 1495 ARG cc_start: 0.7035 (mmm160) cc_final: 0.6760 (ptp90) REVERT: A 1501 PHE cc_start: 0.7185 (t80) cc_final: 0.6904 (t80) REVERT: B 136 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7322 (mtp180) outliers start: 25 outliers final: 13 residues processed: 100 average time/residue: 0.2236 time to fit residues: 32.6479 Evaluate side-chains 94 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.4980 chunk 112 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A1375 GLN B 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10738 Z= 0.221 Angle : 0.641 12.160 14678 Z= 0.302 Chirality : 0.043 0.298 1620 Planarity : 0.004 0.058 1832 Dihedral : 9.350 86.417 1665 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.23 % Rotamer: Outliers : 2.38 % Allowed : 13.06 % Favored : 84.56 % 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: -1.20 (0.24), residues: 1285 helix: 0.48 (0.22), residues: 592 sheet: -1.27 (0.48), residues: 118 loop : -2.09 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1421 HIS 0.005 0.001 HIS A1225 PHE 0.019 0.001 PHE A1370 TYR 0.013 0.001 TYR A1099 ARG 0.004 0.000 ARG A1424 *********************** 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 107 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 1.312 Fit side-chains REVERT: A 300 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8083 (pp) REVERT: A 414 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7945 (t80) REVERT: A 1225 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.7883 (t-90) REVERT: A 1241 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: A 1288 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8687 (t) REVERT: A 1495 ARG cc_start: 0.6982 (mmm160) cc_final: 0.6684 (ptp90) REVERT: A 1501 PHE cc_start: 0.7200 (t80) cc_final: 0.6904 (t80) REVERT: B 136 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7251 (mtp180) outliers start: 25 outliers final: 16 residues processed: 101 average time/residue: 0.2311 time to fit residues: 33.8626 Evaluate side-chains 99 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7735 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10738 Z= 0.223 Angle : 0.638 12.051 14678 Z= 0.300 Chirality : 0.043 0.299 1620 Planarity : 0.004 0.059 1832 Dihedral : 9.082 88.934 1665 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.93 % Favored : 93.00 % Rotamer: Outliers : 2.29 % Allowed : 13.82 % Favored : 83.89 % 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: -1.13 (0.24), residues: 1285 helix: 0.58 (0.22), residues: 587 sheet: -1.26 (0.48), residues: 118 loop : -2.08 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1421 HIS 0.005 0.001 HIS A1225 PHE 0.014 0.001 PHE A 253 TYR 0.012 0.001 TYR A1099 ARG 0.004 0.000 ARG A1424 *********************** 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 106 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 300 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8093 (pp) REVERT: A 414 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7932 (t80) REVERT: A 1225 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.7885 (t-90) REVERT: A 1241 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7127 (m-80) REVERT: A 1288 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8689 (t) REVERT: A 1495 ARG cc_start: 0.6993 (mmm160) cc_final: 0.6694 (ptp90) REVERT: A 1501 PHE cc_start: 0.7177 (t80) cc_final: 0.6900 (t80) REVERT: B 136 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7320 (mtp180) outliers start: 24 outliers final: 15 residues processed: 100 average time/residue: 0.2337 time to fit residues: 33.9279 Evaluate side-chains 100 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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: 0.7684 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10738 Z= 0.168 Angle : 0.600 12.176 14678 Z= 0.281 Chirality : 0.041 0.294 1620 Planarity : 0.004 0.058 1832 Dihedral : 8.416 85.612 1665 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.54 % Rotamer: Outliers : 2.00 % Allowed : 14.30 % Favored : 83.70 % 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: -0.96 (0.24), residues: 1285 helix: 0.70 (0.22), residues: 592 sheet: -1.28 (0.48), residues: 118 loop : -1.97 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1377 HIS 0.004 0.001 HIS A1144 PHE 0.016 0.001 PHE A1370 TYR 0.009 0.001 TYR A1099 ARG 0.004 0.000 ARG A1424 *********************** 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 113 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 300 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8060 (pp) REVERT: A 414 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7886 (t80) REVERT: A 1241 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: A 1288 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8669 (t) REVERT: A 1495 ARG cc_start: 0.7007 (mmm160) cc_final: 0.6684 (ptp90) REVERT: A 1501 PHE cc_start: 0.7158 (t80) cc_final: 0.6856 (t80) REVERT: B 136 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7300 (mtp180) outliers start: 21 outliers final: 13 residues processed: 107 average time/residue: 0.2182 time to fit residues: 34.2249 Evaluate side-chains 99 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 122 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7672 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10738 Z= 0.167 Angle : 0.603 11.943 14678 Z= 0.282 Chirality : 0.042 0.294 1620 Planarity : 0.004 0.054 1832 Dihedral : 8.012 89.546 1665 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.39 % Rotamer: Outliers : 2.00 % Allowed : 14.68 % Favored : 83.32 % 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: -0.79 (0.24), residues: 1285 helix: 0.85 (0.22), residues: 594 sheet: -1.20 (0.48), residues: 118 loop : -1.89 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 HIS 0.004 0.001 HIS A1144 PHE 0.024 0.001 PHE A 329 TYR 0.009 0.001 TYR A1099 ARG 0.004 0.000 ARG A1424 *********************** 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 108 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 300 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8085 (pp) REVERT: A 414 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7886 (t80) REVERT: A 1241 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: A 1288 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8648 (t) REVERT: A 1495 ARG cc_start: 0.6797 (mmm160) cc_final: 0.6512 (ptp90) REVERT: A 1501 PHE cc_start: 0.7159 (t80) cc_final: 0.6879 (t80) REVERT: B 136 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7343 (mtp180) outliers start: 21 outliers final: 16 residues processed: 103 average time/residue: 0.2360 time to fit residues: 35.4253 Evaluate side-chains 105 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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: 0.7676 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10738 Z= 0.175 Angle : 0.609 12.053 14678 Z= 0.285 Chirality : 0.042 0.293 1620 Planarity : 0.004 0.052 1832 Dihedral : 7.770 89.452 1665 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.39 % Rotamer: Outliers : 1.81 % Allowed : 15.25 % Favored : 82.94 % 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: -0.73 (0.24), residues: 1285 helix: 0.91 (0.22), residues: 594 sheet: -1.20 (0.48), residues: 118 loop : -1.87 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 HIS 0.004 0.001 HIS A1144 PHE 0.022 0.001 PHE A 329 TYR 0.009 0.001 TYR A1099 ARG 0.004 0.000 ARG A1424 ********************** 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 105 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 300 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8084 (pp) REVERT: A 414 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7903 (t80) REVERT: A 1241 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: A 1288 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8643 (t) REVERT: A 1495 ARG cc_start: 0.6792 (mmm160) cc_final: 0.6531 (ptp90) REVERT: A 1501 PHE cc_start: 0.7120 (t80) cc_final: 0.6891 (t80) REVERT: B 136 ARG cc_start: 0.7763 (mtp85) cc_final: 0.7347 (mtp180) REVERT: B 179 TYR cc_start: 0.8060 (m-10) cc_final: 0.7769 (m-80) outliers start: 19 outliers final: 14 residues processed: 100 average time/residue: 0.2193 time to fit residues: 32.4494 Evaluate side-chains 103 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 15 optimal weight: 0.0980 chunk 28 optimal weight: 0.0980 chunk 102 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.161993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.127374 restraints weight = 16167.710| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.20 r_work: 0.3650 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10738 Z= 0.154 Angle : 0.588 12.110 14678 Z= 0.274 Chirality : 0.041 0.288 1620 Planarity : 0.004 0.049 1832 Dihedral : 7.186 84.740 1665 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.09 % Rotamer: Outliers : 1.91 % Allowed : 15.06 % Favored : 83.03 % 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: -0.60 (0.24), residues: 1285 helix: 1.05 (0.22), residues: 592 sheet: -1.20 (0.48), residues: 118 loop : -1.82 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1377 HIS 0.005 0.001 HIS A1144 PHE 0.021 0.001 PHE A 329 TYR 0.007 0.001 TYR A1099 ARG 0.003 0.000 ARG A1424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2155.57 seconds wall clock time: 39 minutes 40.88 seconds (2380.88 seconds total)