Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 21 02:42:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g99_29862/08_2023/8g99_29862_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g99_29862/08_2023/8g99_29862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g99_29862/08_2023/8g99_29862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g99_29862/08_2023/8g99_29862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g99_29862/08_2023/8g99_29862_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g99_29862/08_2023/8g99_29862_updated.pdb" } resolution = 2.8 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 2 6.06 5 S 80 5.16 5 C 9632 2.51 5 N 2568 2.21 5 O 2810 1.98 5 H 15109 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1268": "OE1" <-> "OE2" Residue "C PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 30205 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 17195 Classifications: {'peptide': 1063} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1009} Chain breaks: 3 Chain: "B" Number of atoms: 6745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 6745 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 23, 'TRANS': 402} Chain breaks: 2 Chain: "C" Number of atoms: 6255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6255 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 15, 'TRANS': 365} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14369 SG CYS A1280 61.468 53.386 117.661 1.00 79.92 S ATOM 14415 SG CYS A1283 58.004 52.749 118.900 1.00 63.51 S ATOM 14770 SG CYS A1307 58.918 56.142 117.827 1.00 75.11 S ATOM 14842 SG CYS A1312 60.267 54.680 121.000 1.00 90.91 S ATOM 15411 SG CYS A1345 42.636 50.434 76.427 1.00 46.61 S ATOM 15487 SG CYS A1350 40.531 47.429 77.023 1.00 35.85 S ATOM 15786 SG CYS A1368 43.653 47.186 75.020 1.00 43.02 S ATOM 15823 SG CYS A1371 40.786 48.840 73.555 1.00 49.39 S ATOM 28797 SG CYS C 373 46.920 89.519 84.624 1.00 43.99 S ATOM 29045 SG CYS C 390 42.417 91.334 80.057 1.00 32.03 S ATOM 29697 SG CYS C 430 44.610 95.246 84.714 1.00 45.22 S ATOM 27455 SG CYS C 293 40.525 90.220 85.914 1.00 42.93 S Time building chain proxies: 12.89, per 1000 atoms: 0.43 Number of scatterers: 30205 At special positions: 0 Unit cell: (109.88, 120.54, 133.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 4 26.01 S 80 16.00 O 2810 8.00 N 2568 7.00 C 9632 6.00 H 15109 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.78 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 373 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 390 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 293 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 430 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1500 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1283 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1307 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1280 " pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1371 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1368 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1350 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1345 " Number of angles added : 12 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 11 sheets defined 40.1% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 410 through 419 Processing helix chain 'A' and resid 421 through 424 No H-bonds generated for 'chain 'A' and resid 421 through 424' Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 643 through 654 Processing helix chain 'A' and resid 659 through 662 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 725 through 728 No H-bonds generated for 'chain 'A' and resid 725 through 728' Processing helix chain 'A' and resid 735 through 759 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 788 through 799 Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'A' and resid 906 through 925 Processing helix chain 'A' and resid 932 through 957 removed outlier: 4.774A pdb=" N TYR A 953 " --> pdb=" O ALA A 949 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY A 954 " --> pdb=" O ASN A 950 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 989 Processing helix chain 'A' and resid 1011 through 1028 removed outlier: 3.741A pdb=" N SER A1028 " --> pdb=" O GLU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1095 Processing helix chain 'A' and resid 1101 through 1121 Processing helix chain 'A' and resid 1126 through 1129 Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1145 through 1147 No H-bonds generated for 'chain 'A' and resid 1145 through 1147' Processing helix chain 'A' and resid 1149 through 1160 Processing helix chain 'A' and resid 1191 through 1197 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1212 through 1220 removed outlier: 4.340A pdb=" N ILE A1219 " --> pdb=" O VAL A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1235 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1252 through 1258 Processing helix chain 'A' and resid 1266 through 1269 No H-bonds generated for 'chain 'A' and resid 1266 through 1269' Processing helix chain 'A' and resid 1297 through 1299 No H-bonds generated for 'chain 'A' and resid 1297 through 1299' Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1320 through 1339 Processing helix chain 'A' and resid 1382 through 1396 removed outlier: 3.759A pdb=" N PHE A1396 " --> pdb=" O TYR A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1403 Processing helix chain 'A' and resid 1408 through 1414 Processing helix chain 'A' and resid 1420 through 1439 removed outlier: 3.548A pdb=" N THR A1432 " --> pdb=" O LYS A1428 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A1433 " --> pdb=" O LEU A1429 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A1439 " --> pdb=" O GLN A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1450 No H-bonds generated for 'chain 'A' and resid 1447 through 1450' Processing helix chain 'B' and resid 213 through 235 Processing helix chain 'B' and resid 276 through 279 No H-bonds generated for 'chain 'B' and resid 276 through 279' Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 358 through 370 Processing helix chain 'B' and resid 387 through 390 No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 476 through 481 Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'C' and resid 41 through 64 Processing helix chain 'C' and resid 70 through 83 Processing helix chain 'C' and resid 96 through 115 removed outlier: 3.617A pdb=" N PHE C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 140 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 220 through 242 Processing helix chain 'C' and resid 244 through 247 No H-bonds generated for 'chain 'C' and resid 244 through 247' Processing helix chain 'C' and resid 250 through 256 Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 279 through 288 removed outlier: 4.079A pdb=" N ASP C 283 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 303 removed outlier: 3.696A pdb=" N LEU C 297 " --> pdb=" O CYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 326 through 339 Processing helix chain 'C' and resid 344 through 349 Processing helix chain 'C' and resid 352 through 359 Processing helix chain 'C' and resid 373 through 378 Processing helix chain 'C' and resid 391 through 394 No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 397 through 407 Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 450 through 460 Processing sheet with id= A, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.543A pdb=" N SER A 497 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TRP A 366 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 348 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 516 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N SER A 379 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A 518 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 385 through 390 Processing sheet with id= C, first strand: chain 'A' and resid 689 through 692 removed outlier: 6.512A pdb=" N VAL A 547 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE A 557 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A 558 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 849 through 851 removed outlier: 6.552A pdb=" N LYS A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1035 through 1040 removed outlier: 3.923A pdb=" N ASP A1035 " --> pdb=" O ASP A 859 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 857 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE A1039 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 855 " --> pdb=" O ILE A1039 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN A1005 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL A 994 " --> pdb=" O ASN A1005 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1131 through 1134 Processing sheet with id= G, first strand: chain 'A' and resid 1276 through 1279 Processing sheet with id= H, first strand: chain 'A' and resid 1343 through 1345 Processing sheet with id= I, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.257A pdb=" N VAL B 537 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N THR B 472 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 539 " --> pdb=" O THR B 472 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 555 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL B 540 " --> pdb=" O ILE B 555 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE B 557 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 283 through 285 removed outlier: 6.347A pdb=" N THR B 307 " --> pdb=" O PRO B 316 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 453 through 456 removed outlier: 6.510A pdb=" N LEU B 420 " --> pdb=" O HIS B 454 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B 456 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE B 422 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N CYS B 346 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N THR B 570 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 592 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG B 597 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 170 " --> pdb=" O ARG B 597 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1737 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: 11.97 Time building geometry restraints manager: 26.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 15078 1.13 - 1.42: 6317 1.42 - 1.70: 9019 1.70 - 1.99: 109 1.99 - 2.28: 12 Bond restraints: 30535 Sorted by residual: bond pdb=" CA ARG B 371 " pdb=" C ARG B 371 " ideal model delta sigma weight residual 1.531 1.523 0.009 7.40e-03 1.83e+04 1.36e+00 bond pdb=" CA ARG C 334 " pdb=" C ARG C 334 " ideal model delta sigma weight residual 1.524 1.511 0.014 1.28e-02 6.10e+03 1.17e+00 bond pdb=" CA PHE C 126 " pdb=" C PHE C 126 " ideal model delta sigma weight residual 1.524 1.510 0.014 1.32e-02 5.74e+03 1.07e+00 bond pdb=" CA LEU C 225 " pdb=" C LEU C 225 " ideal model delta sigma weight residual 1.523 1.511 0.012 1.30e-02 5.92e+03 8.79e-01 bond pdb=" CA ILE C 127 " pdb=" C ILE C 127 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.22e-02 6.72e+03 8.22e-01 ... (remaining 30530 not shown) Histogram of bond angle deviations from ideal: 73.64 - 85.71: 12 85.71 - 97.79: 0 97.79 - 109.87: 23705 109.87 - 121.94: 26393 121.94 - 134.02: 5195 Bond angle restraints: 55305 Sorted by residual: angle pdb=" N GLY A 363 " pdb=" CA GLY A 363 " pdb=" C GLY A 363 " ideal model delta sigma weight residual 111.08 114.78 -3.70 1.62e+00 3.81e-01 5.23e+00 angle pdb=" C LEU A 589 " pdb=" N ASN A 590 " pdb=" CA ASN A 590 " ideal model delta sigma weight residual 122.93 119.60 3.33 1.51e+00 4.39e-01 4.88e+00 angle pdb=" N LYS C 104 " pdb=" CA LYS C 104 " pdb=" C LYS C 104 " ideal model delta sigma weight residual 111.37 107.82 3.55 1.64e+00 3.72e-01 4.69e+00 angle pdb=" N ARG C 334 " pdb=" CA ARG C 334 " pdb=" C ARG C 334 " ideal model delta sigma weight residual 111.02 108.42 2.60 1.22e+00 6.72e-01 4.53e+00 angle pdb=" N THR C 338 " pdb=" CA THR C 338 " pdb=" C THR C 338 " ideal model delta sigma weight residual 112.38 110.00 2.38 1.22e+00 6.72e-01 3.82e+00 ... (remaining 55300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 11038 17.86 - 35.71: 906 35.71 - 53.57: 244 53.57 - 71.42: 72 71.42 - 89.28: 27 Dihedral angle restraints: 12287 sinusoidal: 5811 harmonic: 6476 Sorted by residual: dihedral pdb=" CA ASP A 632 " pdb=" CB ASP A 632 " pdb=" CG ASP A 632 " pdb=" OD1 ASP A 632 " ideal model delta sinusoidal sigma weight residual -30.00 -86.10 56.10 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB GLU B 273 " pdb=" CG GLU B 273 " pdb=" CD GLU B 273 " pdb=" OE1 GLU B 273 " ideal model delta sinusoidal sigma weight residual 0.00 -89.28 89.28 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 786 " pdb=" CG GLU A 786 " pdb=" CD GLU A 786 " pdb=" OE1 GLU A 786 " ideal model delta sinusoidal sigma weight residual 0.00 -88.82 88.82 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1381 0.027 - 0.053: 605 0.053 - 0.080: 162 0.080 - 0.106: 109 0.106 - 0.133: 52 Chirality restraints: 2309 Sorted by residual: chirality pdb=" CA ILE B 303 " pdb=" N ILE B 303 " pdb=" C ILE B 303 " pdb=" CB ILE B 303 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE A 501 " pdb=" N ILE A 501 " pdb=" C ILE A 501 " pdb=" CB ILE A 501 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE A1004 " pdb=" N ILE A1004 " pdb=" C ILE A1004 " pdb=" CB ILE A1004 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 2306 not shown) Planarity restraints: 4451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 334 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C ARG C 334 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG C 334 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 335 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 104 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.39e+00 pdb=" C LYS C 104 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS C 104 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP C 105 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 332 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C PHE C 332 " -0.038 2.00e-02 2.50e+03 pdb=" O PHE C 332 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP C 333 " 0.013 2.00e-02 2.50e+03 ... (remaining 4448 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 595 2.12 - 2.74: 54645 2.74 - 3.36: 86910 3.36 - 3.98: 112338 3.98 - 4.60: 176013 Nonbonded interactions: 430501 Sorted by model distance: nonbonded pdb=" O LEU B 525 " pdb=" HG1 THR B 529 " model vdw 1.497 1.850 nonbonded pdb=" O LEU A1135 " pdb=" H GLY A1168 " model vdw 1.554 1.850 nonbonded pdb="HH11 ARG A 667 " pdb=" O ASN A 683 " model vdw 1.591 1.850 nonbonded pdb=" O GLN A 397 " pdb=" H GLY A 401 " model vdw 1.596 1.850 nonbonded pdb="HH21 ARG C 51 " pdb=" OD1 ASP C 105 " model vdw 1.639 1.850 ... (remaining 430496 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: 5.070 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: 0.450 Extract box with map and model: 15.720 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 112.300 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 : 0.003 0.031 15426 Z= 0.206 Angle : 0.467 4.553 20863 Z= 0.258 Chirality : 0.039 0.133 2309 Planarity : 0.003 0.031 2682 Dihedral : 16.851 89.277 5844 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1855 helix: 0.75 (0.19), residues: 796 sheet: 0.78 (0.31), residues: 259 loop : 0.03 (0.23), residues: 800 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 4.1067 time to fit residues: 764.1496 Evaluate side-chains 67 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 733 ASN A 861 ASN A 869 GLN A 937 GLN A1026 ASN A1435 GLN C 331 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 15426 Z= 0.191 Angle : 0.499 6.022 20863 Z= 0.253 Chirality : 0.039 0.139 2309 Planarity : 0.003 0.044 2682 Dihedral : 3.868 21.201 2041 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.26 % Favored : 97.68 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1855 helix: 1.65 (0.19), residues: 794 sheet: 0.83 (0.31), residues: 258 loop : 0.05 (0.23), residues: 803 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 82 average time/residue: 3.1612 time to fit residues: 286.3590 Evaluate side-chains 61 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 2.338 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 3.1712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 0.0970 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 ASN C 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 15426 Z= 0.185 Angle : 0.477 5.957 20863 Z= 0.241 Chirality : 0.039 0.138 2309 Planarity : 0.003 0.030 2682 Dihedral : 3.771 20.132 2041 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.20), residues: 1855 helix: 2.01 (0.19), residues: 793 sheet: 0.83 (0.31), residues: 258 loop : 0.09 (0.23), residues: 804 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 73 average time/residue: 3.0496 time to fit residues: 247.8025 Evaluate side-chains 61 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 2.686 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 3.3053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 ASN A1107 ASN A1193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15426 Z= 0.208 Angle : 0.476 7.288 20863 Z= 0.239 Chirality : 0.039 0.131 2309 Planarity : 0.003 0.034 2682 Dihedral : 3.715 19.396 2041 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.20), residues: 1855 helix: 2.17 (0.19), residues: 788 sheet: 0.84 (0.31), residues: 260 loop : 0.16 (0.23), residues: 807 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 70 average time/residue: 3.1903 time to fit residues: 247.2869 Evaluate side-chains 60 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 2.274 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 2.8751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 15426 Z= 0.357 Angle : 0.509 5.355 20863 Z= 0.259 Chirality : 0.040 0.130 2309 Planarity : 0.003 0.030 2682 Dihedral : 3.850 18.365 2041 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.20), residues: 1855 helix: 2.12 (0.19), residues: 787 sheet: 0.73 (0.31), residues: 266 loop : 0.13 (0.22), residues: 802 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 2.8692 time to fit residues: 202.6647 Evaluate side-chains 58 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 2.442 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.4733 time to fit residues: 3.8639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.8735 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 15426 Z= 0.251 Angle : 0.477 5.203 20863 Z= 0.243 Chirality : 0.040 0.133 2309 Planarity : 0.003 0.046 2682 Dihedral : 3.786 17.940 2041 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1855 helix: 2.19 (0.19), residues: 788 sheet: 0.78 (0.31), residues: 262 loop : 0.18 (0.23), residues: 805 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 3.1569 time to fit residues: 214.8399 Evaluate side-chains 57 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 2.468 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 2.9826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 180 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.8739 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 15426 Z= 0.258 Angle : 0.481 8.331 20863 Z= 0.243 Chirality : 0.039 0.132 2309 Planarity : 0.003 0.027 2682 Dihedral : 3.774 17.818 2041 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.20), residues: 1855 helix: 2.21 (0.19), residues: 788 sheet: 0.74 (0.31), residues: 262 loop : 0.21 (0.22), residues: 805 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 3.1094 time to fit residues: 215.2789 Evaluate side-chains 55 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 2.465 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 3.1635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 0.0060 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15426 Z= 0.195 Angle : 0.468 6.553 20863 Z= 0.236 Chirality : 0.039 0.135 2309 Planarity : 0.003 0.027 2682 Dihedral : 3.714 16.945 2041 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.20), residues: 1855 helix: 2.27 (0.19), residues: 790 sheet: 0.85 (0.32), residues: 251 loop : 0.27 (0.23), residues: 814 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 57 average time/residue: 3.2573 time to fit residues: 207.5910 Evaluate side-chains 57 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 2.276 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 2.9240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15426 Z= 0.213 Angle : 0.469 6.104 20863 Z= 0.236 Chirality : 0.039 0.131 2309 Planarity : 0.003 0.027 2682 Dihedral : 3.676 16.329 2041 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.20), residues: 1855 helix: 2.34 (0.19), residues: 784 sheet: 0.85 (0.32), residues: 251 loop : 0.29 (0.22), residues: 820 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 58 average time/residue: 3.3009 time to fit residues: 213.2518 Evaluate side-chains 57 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 2.273 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 3.0357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 123 optimal weight: 0.0970 chunk 186 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15426 Z= 0.163 Angle : 0.458 5.936 20863 Z= 0.230 Chirality : 0.039 0.133 2309 Planarity : 0.003 0.028 2682 Dihedral : 3.615 15.442 2041 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.20), residues: 1855 helix: 2.44 (0.19), residues: 782 sheet: 0.84 (0.32), residues: 251 loop : 0.32 (0.22), residues: 822 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 3.2148 time to fit residues: 203.5716 Evaluate side-chains 54 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 2.393 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 3.0065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.048648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.036688 restraints weight = 134799.843| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 2.95 r_work: 0.2391 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2277 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15426 Z= 0.266 Angle : 0.483 6.908 20863 Z= 0.243 Chirality : 0.039 0.130 2309 Planarity : 0.003 0.027 2682 Dihedral : 3.650 16.470 2041 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.20), residues: 1855 helix: 2.37 (0.19), residues: 784 sheet: 0.80 (0.32), residues: 254 loop : 0.33 (0.22), residues: 817 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7233.28 seconds wall clock time: 128 minutes 51.62 seconds (7731.62 seconds total)