Starting phenix.real_space_refine on Sat Dec 9 12:57:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/12_2023/7syf_25524.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/12_2023/7syf_25524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/12_2023/7syf_25524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/12_2023/7syf_25524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/12_2023/7syf_25524.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syf_25524/12_2023/7syf_25524.pdb" } resolution = 4.2 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= 0.016 sd= 0.092 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 7024 2.51 5 N 1942 2.21 5 O 2070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 78": "NH1" <-> "NH2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A GLU 858": "OE1" <-> "OE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 899": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 928": "OE1" <-> "OE2" Residue "A GLU 939": "OE1" <-> "OE2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A GLU 1074": "OE1" <-> "OE2" Residue "A GLU 1247": "OE1" <-> "OE2" Residue "A GLU 1265": "OE1" <-> "OE2" Residue "A GLU 1280": "OE1" <-> "OE2" Residue "A GLU 1301": "OE1" <-> "OE2" Residue "A GLU 1340": "OE1" <-> "OE2" Residue "A GLU 1355": "OE1" <-> "OE2" Residue "A GLU 1357": "OE1" <-> "OE2" Residue "A GLU 1358": "OE1" <-> "OE2" Residue "A ARG 1365": "NH1" <-> "NH2" Residue "A GLU 1369": "OE1" <-> "OE2" Residue "A GLU 1397": "OE1" <-> "OE2" Residue "A GLU 1405": "OE1" <-> "OE2" Residue "A GLU 1431": "OE1" <-> "OE2" Residue "A GLU 1456": "OE1" <-> "OE2" Residue "A GLU 1473": "OE1" <-> "OE2" Residue "A GLU 1476": "OE1" <-> "OE2" Residue "A GLU 1487": "OE1" <-> "OE2" Residue "A GLU 1499": "OE1" <-> "OE2" Residue "A GLU 1514": "OE1" <-> "OE2" Residue "A ARG 1534": "NH1" <-> "NH2" Residue "A GLU 1541": "OE1" <-> "OE2" Residue "A GLU 1570": "OE1" <-> "OE2" Residue "A ARG 1621": "NH1" <-> "NH2" Residue "A GLU 1628": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11108 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1391, 11108 Classifications: {'peptide': 1391} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 47, 'TRANS': 1340} Chain breaks: 7 Time building chain proxies: 5.82, per 1000 atoms: 0.52 Number of scatterers: 11108 At special positions: 0 Unit cell: (111.688, 123.799, 139.947, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2070 8.00 N 1942 7.00 C 7024 6.00 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: 3.65 Conformation dependent library (CDL) restraints added in 2.1 seconds 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 58.6% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 42 through 82 removed outlier: 3.715A pdb=" N HIS A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 121 removed outlier: 3.511A pdb=" N SER A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASN A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 removed outlier: 4.282A pdb=" N ASP A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 165 removed outlier: 3.780A pdb=" N TYR A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 180 removed outlier: 3.673A pdb=" N MET A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 193 through 213 Proline residue: A 203 - end of helix removed outlier: 3.667A pdb=" N ARG A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 237 removed outlier: 4.610A pdb=" N ALA A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 256 removed outlier: 3.709A pdb=" N LEU A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.646A pdb=" N ILE A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 421 Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 459 through 473 removed outlier: 3.539A pdb=" N GLY A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 523 removed outlier: 3.512A pdb=" N ASP A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 560 through 574 Processing helix chain 'A' and resid 596 through 603 removed outlier: 3.906A pdb=" N MET A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 680 through 694 removed outlier: 3.515A pdb=" N SER A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 Processing helix chain 'A' and resid 763 through 769 Processing helix chain 'A' and resid 771 through 778 Processing helix chain 'A' and resid 779 through 782 removed outlier: 4.135A pdb=" N LEU A 782 " --> pdb=" O GLU A 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 779 through 782' Processing helix chain 'A' and resid 791 through 806 Processing helix chain 'A' and resid 878 through 908 Processing helix chain 'A' and resid 913 through 946 Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 1064 through 1068 Processing helix chain 'A' and resid 1069 through 1108 removed outlier: 3.622A pdb=" N ARG A1073 " --> pdb=" O LYS A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1237 removed outlier: 4.925A pdb=" N LEU A1235 " --> pdb=" O SER A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1248 Processing helix chain 'A' and resid 1256 through 1263 Processing helix chain 'A' and resid 1263 through 1281 Processing helix chain 'A' and resid 1284 through 1315 Processing helix chain 'A' and resid 1316 through 1346 Processing helix chain 'A' and resid 1353 through 1357 removed outlier: 3.565A pdb=" N GLU A1357 " --> pdb=" O GLY A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1375 Processing helix chain 'A' and resid 1389 through 1407 removed outlier: 4.241A pdb=" N VAL A1401 " --> pdb=" O GLU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1450 Processing helix chain 'A' and resid 1452 through 1457 Processing helix chain 'A' and resid 1480 through 1517 Processing helix chain 'A' and resid 1521 through 1551 removed outlier: 4.216A pdb=" N ARG A1534 " --> pdb=" O ASP A1530 " (cutoff:3.500A) Proline residue: A1535 - end of helix Processing helix chain 'A' and resid 1563 through 1576 Processing helix chain 'A' and resid 1588 through 1606 Processing helix chain 'A' and resid 1609 through 1611 No H-bonds generated for 'chain 'A' and resid 1609 through 1611' Processing helix chain 'A' and resid 1612 through 1624 Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 4.133A pdb=" N LEU A1630 " --> pdb=" O ARG A1626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 258 removed outlier: 3.559A pdb=" N PHE A 327 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE A 327 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS A 302 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN A 287 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU A 279 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A 289 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR A 277 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE A 291 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN A 275 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 293 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 431 removed outlier: 5.299A pdb=" N LYS A 429 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 440 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N LYS A 440 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE A 494 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 530 through 533 removed outlier: 5.048A pdb=" N ARG A 532 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS A 540 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N SER A 541 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE A 595 " --> pdb=" O SER A 541 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 668 through 671 removed outlier: 6.337A pdb=" N LEU A 701 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE A 671 " --> pdb=" O ARG A 699 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG A 699 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE A 615 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL A 860 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU A 617 " --> pdb=" O GLU A 858 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU A 858 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 619 " --> pdb=" O VAL A 856 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N HIS A 868 " --> pdb=" O SER A 980 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A1579 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS A1583 " --> pdb=" O MET A1025 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A1376 " --> pdb=" O HIS A1464 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA A1466 " --> pdb=" O VAL A1376 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A1378 " --> pdb=" O ALA A1466 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE A1468 " --> pdb=" O LEU A1378 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N CYS A1380 " --> pdb=" O PHE A1468 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR A1410 " --> pdb=" O VAL A1439 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N PHE A1441 " --> pdb=" O THR A1410 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A1412 " --> pdb=" O PHE A1441 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU A1443 " --> pdb=" O SER A1412 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS A1414 " --> pdb=" O LEU A1443 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 637 through 642 removed outlier: 6.651A pdb=" N ASP A 638 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 713 removed outlier: 6.485A pdb=" N THR A 843 " --> pdb=" O VAL A 754 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 754 " --> pdb=" O THR A 843 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR A 845 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 721 through 724 removed outlier: 6.672A pdb=" N GLN A 722 " --> pdb=" O TYR A 732 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 2007 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: 4.35 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2166 1.32 - 1.45: 2626 1.45 - 1.57: 6413 1.57 - 1.70: 0 1.70 - 1.83: 105 Bond restraints: 11310 Sorted by residual: bond pdb=" C PHE A1260 " pdb=" N LYS A1261 " ideal model delta sigma weight residual 1.335 1.571 -0.237 1.25e-02 6.40e+03 3.59e+02 bond pdb=" C ARG A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 1.331 1.490 -0.159 1.42e-02 4.96e+03 1.25e+02 bond pdb=" C GLU A 619 " pdb=" N ASN A 620 " ideal model delta sigma weight residual 1.330 1.253 0.077 1.38e-02 5.25e+03 3.14e+01 bond pdb=" C VAL A 618 " pdb=" N GLU A 619 " ideal model delta sigma weight residual 1.332 1.260 0.072 1.40e-02 5.10e+03 2.66e+01 bond pdb=" C LEU A 227 " pdb=" N GLN A 228 " ideal model delta sigma weight residual 1.335 1.387 -0.053 1.31e-02 5.83e+03 1.61e+01 ... (remaining 11305 not shown) Histogram of bond angle deviations from ideal: 96.93 - 104.61: 153 104.61 - 112.30: 4866 112.30 - 119.98: 5401 119.98 - 127.67: 4763 127.67 - 135.35: 79 Bond angle restraints: 15262 Sorted by residual: angle pdb=" C PHE A1260 " pdb=" N LYS A1261 " pdb=" CA LYS A1261 " ideal model delta sigma weight residual 120.54 109.71 10.83 1.35e+00 5.49e-01 6.44e+01 angle pdb=" N TYR A 539 " pdb=" CA TYR A 539 " pdb=" C TYR A 539 " ideal model delta sigma weight residual 109.95 99.43 10.52 1.59e+00 3.96e-01 4.38e+01 angle pdb=" CA PHE A 70 " pdb=" CB PHE A 70 " pdb=" CG PHE A 70 " ideal model delta sigma weight residual 113.80 120.01 -6.21 1.00e+00 1.00e+00 3.86e+01 angle pdb=" N ILE A 103 " pdb=" CA ILE A 103 " pdb=" CB ILE A 103 " ideal model delta sigma weight residual 110.51 117.25 -6.74 1.11e+00 8.12e-01 3.69e+01 angle pdb=" O PHE A1260 " pdb=" C PHE A1260 " pdb=" N LYS A1261 " ideal model delta sigma weight residual 122.12 128.45 -6.33 1.06e+00 8.90e-01 3.57e+01 ... (remaining 15257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 6298 17.72 - 35.44: 481 35.44 - 53.15: 99 53.15 - 70.87: 35 70.87 - 88.59: 11 Dihedral angle restraints: 6924 sinusoidal: 2859 harmonic: 4065 Sorted by residual: dihedral pdb=" CA LEU A1068 " pdb=" C LEU A1068 " pdb=" N LYS A1069 " pdb=" CA LYS A1069 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA LEU A 700 " pdb=" C LEU A 700 " pdb=" N LEU A 701 " pdb=" CA LEU A 701 " ideal model delta harmonic sigma weight residual 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ALA A 283 " pdb=" C ALA A 283 " pdb=" N GLY A 284 " pdb=" CA GLY A 284 " ideal model delta harmonic sigma weight residual -180.00 -151.65 -28.35 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 6921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1210 0.098 - 0.196: 426 0.196 - 0.294: 56 0.294 - 0.392: 11 0.392 - 0.490: 6 Chirality restraints: 1709 Sorted by residual: chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 1.94 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CA ARG A 303 " pdb=" N ARG A 303 " pdb=" C ARG A 303 " pdb=" CB ARG A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CA ARG A 198 " pdb=" N ARG A 198 " pdb=" C ARG A 198 " pdb=" CB ARG A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.26e+00 ... (remaining 1706 not shown) Planarity restraints: 1973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 260 " -0.134 2.00e-02 2.50e+03 7.38e-02 1.36e+02 pdb=" CG TRP A 260 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 260 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 260 " 0.108 2.00e-02 2.50e+03 pdb=" NE1 TRP A 260 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 260 " 0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP A 260 " 0.102 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 260 " -0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 260 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 260 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 787 " -0.093 2.00e-02 2.50e+03 5.11e-02 6.52e+01 pdb=" CG TRP A 787 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 787 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP A 787 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP A 787 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP A 787 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 787 " 0.074 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 787 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 787 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP A 787 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1020 " 0.084 2.00e-02 2.50e+03 6.25e-02 5.85e+01 pdb=" CG HIS A1020 " -0.095 2.00e-02 2.50e+03 pdb=" ND1 HIS A1020 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS A1020 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 HIS A1020 " 0.034 2.00e-02 2.50e+03 pdb=" NE2 HIS A1020 " 0.055 2.00e-02 2.50e+03 ... (remaining 1970 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 4664 2.95 - 3.44: 11727 3.44 - 3.92: 18891 3.92 - 4.41: 21061 4.41 - 4.90: 34498 Nonbonded interactions: 90841 Sorted by model distance: nonbonded pdb=" N TYR A 539 " pdb=" O TYR A 539 " model vdw 2.460 2.496 nonbonded pdb=" OG SER A 458 " pdb=" OE2 GLU A 462 " model vdw 2.478 2.440 nonbonded pdb=" OG SER A1569 " pdb=" OE2 GLU A1597 " model vdw 2.512 2.440 nonbonded pdb=" ND1 HIS A 77 " pdb=" NH2 ARG A 80 " model vdw 2.520 3.200 nonbonded pdb=" OG1 THR A 354 " pdb=" OE1 GLU A1092 " model vdw 2.564 2.440 ... (remaining 90836 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 group one per residue 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: 0.150 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: 1.410 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.140 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 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 : 0.013 0.237 11310 Z= 0.829 Angle : 1.861 10.834 15262 Z= 1.269 Chirality : 0.098 0.490 1709 Planarity : 0.015 0.128 1973 Dihedral : 14.320 88.585 4288 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.31 % Allowed : 3.60 % Favored : 95.09 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 6.00 % 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: 1375 helix: -1.07 (0.15), residues: 766 sheet: -0.80 (0.39), residues: 153 loop : -0.65 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.032 TRP A 260 HIS 0.019 0.005 HIS A 579 PHE 0.067 0.014 PHE A 593 TYR 0.097 0.016 TYR A 191 ARG 0.009 0.001 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 409 time to evaluate : 1.215 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 revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 418 average time/residue: 0.3007 time to fit residues: 166.2916 Evaluate side-chains 282 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 279 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1342 time to fit residues: 2.5377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 110 HIS A 133 ASN A 228 GLN A 256 HIS A 393 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN A 722 GLN A 790 HIS ** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 GLN A1379 HIS A1415 GLN ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11310 Z= 0.283 Angle : 0.706 9.657 15262 Z= 0.381 Chirality : 0.044 0.250 1709 Planarity : 0.006 0.117 1973 Dihedral : 6.200 76.632 1510 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Rotamer: Outliers : 0.16 % Allowed : 3.68 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.30 (0.22), residues: 1375 helix: 0.78 (0.18), residues: 766 sheet: -0.66 (0.38), residues: 162 loop : -0.26 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 369 HIS 0.008 0.002 HIS A1219 PHE 0.025 0.003 PHE A 70 TYR 0.038 0.003 TYR A1512 ARG 0.010 0.001 ARG A1393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 1.162 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 309 average time/residue: 0.2694 time to fit residues: 113.5008 Evaluate side-chains 243 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1392 time to fit residues: 1.8990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN A1101 ASN A1233 ASN A1284 ASN A1287 ASN ** A1502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1537 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11310 Z= 0.222 Angle : 0.635 9.889 15262 Z= 0.337 Chirality : 0.042 0.236 1709 Planarity : 0.004 0.043 1973 Dihedral : 5.769 76.583 1510 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.84 (0.22), residues: 1375 helix: 1.27 (0.18), residues: 771 sheet: -0.66 (0.37), residues: 159 loop : -0.07 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 450 HIS 0.004 0.001 HIS A 77 PHE 0.020 0.002 PHE A 593 TYR 0.028 0.002 TYR A 325 ARG 0.008 0.001 ARG A1604 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 1.499 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: 1 outliers final: 1 residues processed: 297 average time/residue: 0.2708 time to fit residues: 110.1045 Evaluate side-chains 249 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1540 time to fit residues: 1.9218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 chunk 84 optimal weight: 0.0060 chunk 126 optimal weight: 0.9990 chunk 134 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 ASN A1415 GLN ** A1502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1633 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11310 Z= 0.194 Angle : 0.602 8.509 15262 Z= 0.314 Chirality : 0.041 0.225 1709 Planarity : 0.004 0.076 1973 Dihedral : 5.489 75.381 1510 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.08 % Allowed : 2.62 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 1.09 (0.23), residues: 1375 helix: 1.48 (0.18), residues: 769 sheet: -0.52 (0.38), residues: 158 loop : 0.02 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 369 HIS 0.004 0.001 HIS A 853 PHE 0.019 0.002 PHE A1083 TYR 0.021 0.002 TYR A 300 ARG 0.006 0.001 ARG A1534 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 1.330 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 revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 287 average time/residue: 0.2792 time to fit residues: 109.9603 Evaluate side-chains 238 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1442 time to fit residues: 2.1435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 228 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 ASN A1250 HIS A1287 ASN A1415 GLN A1435 GLN A1490 GLN ** A1502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11310 Z= 0.239 Angle : 0.654 9.493 15262 Z= 0.336 Chirality : 0.042 0.260 1709 Planarity : 0.004 0.038 1973 Dihedral : 5.492 74.243 1510 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.16 % Allowed : 2.13 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 1.00 (0.23), residues: 1375 helix: 1.46 (0.18), residues: 776 sheet: -0.50 (0.38), residues: 154 loop : -0.17 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 369 HIS 0.005 0.001 HIS A 77 PHE 0.020 0.002 PHE A1226 TYR 0.046 0.002 TYR A1512 ARG 0.011 0.001 ARG A1454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 287 time to evaluate : 1.273 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 revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 289 average time/residue: 0.2776 time to fit residues: 109.4392 Evaluate side-chains 246 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1352 time to fit residues: 1.9547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.0010 chunk 33 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 11 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 ASN ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1381 GLN A1415 GLN A1502 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11310 Z= 0.200 Angle : 0.653 10.873 15262 Z= 0.332 Chirality : 0.042 0.233 1709 Planarity : 0.005 0.067 1973 Dihedral : 5.364 71.938 1510 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.16 % Allowed : 1.55 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 1.04 (0.23), residues: 1375 helix: 1.49 (0.18), residues: 769 sheet: -0.31 (0.38), residues: 154 loop : -0.20 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 787 HIS 0.004 0.001 HIS A 110 PHE 0.015 0.001 PHE A1083 TYR 0.039 0.002 TYR A1512 ARG 0.011 0.001 ARG A1271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 1.149 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: 2 outliers final: 1 residues processed: 274 average time/residue: 0.2815 time to fit residues: 105.7226 Evaluate side-chains 235 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.262 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1383 time to fit residues: 1.9795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11310 Z= 0.200 Angle : 0.641 8.367 15262 Z= 0.327 Chirality : 0.042 0.300 1709 Planarity : 0.004 0.055 1973 Dihedral : 5.262 69.202 1510 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.16 % Allowed : 0.90 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 1.09 (0.23), residues: 1375 helix: 1.53 (0.18), residues: 772 sheet: -0.34 (0.38), residues: 154 loop : -0.19 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 369 HIS 0.008 0.001 HIS A 362 PHE 0.015 0.002 PHE A1083 TYR 0.041 0.002 TYR A1512 ARG 0.012 0.001 ARG A1454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 268 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 270 average time/residue: 0.2705 time to fit residues: 101.2124 Evaluate side-chains 232 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1450 time to fit residues: 2.0234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 ASN ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11310 Z= 0.322 Angle : 0.744 9.540 15262 Z= 0.391 Chirality : 0.046 0.327 1709 Planarity : 0.005 0.045 1973 Dihedral : 5.615 66.793 1510 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.68 (0.23), residues: 1375 helix: 1.23 (0.18), residues: 773 sheet: -0.42 (0.39), residues: 148 loop : -0.47 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 369 HIS 0.008 0.002 HIS A 77 PHE 0.020 0.002 PHE A1226 TYR 0.023 0.003 TYR A 202 ARG 0.013 0.001 ARG A1271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.271 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: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2692 time to fit residues: 100.8338 Evaluate side-chains 233 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1329 GLN A1579 GLN ** A1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.6886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11310 Z= 0.210 Angle : 0.690 8.363 15262 Z= 0.358 Chirality : 0.044 0.350 1709 Planarity : 0.005 0.072 1973 Dihedral : 5.418 63.533 1510 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.08 % Allowed : 0.41 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.84 (0.23), residues: 1375 helix: 1.32 (0.19), residues: 765 sheet: -0.25 (0.39), residues: 147 loop : -0.33 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 369 HIS 0.005 0.001 HIS A 110 PHE 0.029 0.002 PHE A 919 TYR 0.032 0.002 TYR A 202 ARG 0.010 0.001 ARG A1534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 1.202 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 revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.2705 time to fit residues: 103.8473 Evaluate side-chains 238 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 0.0670 chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 0.0770 chunk 117 optimal weight: 6.9990 overall best weight: 1.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 ASN A1297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11310 Z= 0.228 Angle : 0.716 9.706 15262 Z= 0.368 Chirality : 0.044 0.284 1709 Planarity : 0.005 0.043 1973 Dihedral : 5.400 60.113 1510 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.16 % Allowed : 0.33 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.75 (0.23), residues: 1375 helix: 1.24 (0.18), residues: 764 sheet: -0.19 (0.40), residues: 145 loop : -0.38 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 369 HIS 0.005 0.001 HIS A 362 PHE 0.021 0.002 PHE A 919 TYR 0.028 0.002 TYR A 202 ARG 0.011 0.001 ARG A1534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 267 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 269 average time/residue: 0.2551 time to fit residues: 96.2048 Evaluate side-chains 237 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 16 optimal weight: 0.0060 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 351 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.138275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.119849 restraints weight = 32747.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.122922 restraints weight = 21571.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.125159 restraints weight = 15362.058| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.7227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11310 Z= 0.203 Angle : 0.709 9.015 15262 Z= 0.365 Chirality : 0.044 0.277 1709 Planarity : 0.004 0.044 1973 Dihedral : 5.220 55.095 1510 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.80 (0.23), residues: 1375 helix: 1.25 (0.18), residues: 766 sheet: -0.14 (0.41), residues: 149 loop : -0.32 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 369 HIS 0.005 0.001 HIS A 77 PHE 0.023 0.002 PHE A 919 TYR 0.031 0.002 TYR A1573 ARG 0.010 0.001 ARG A1534 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2705.35 seconds wall clock time: 49 minutes 49.04 seconds (2989.04 seconds total)