Starting phenix.real_space_refine on Sat Dec 9 04:59:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/12_2023/7ui6_26540.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/12_2023/7ui6_26540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/12_2023/7ui6_26540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/12_2023/7ui6_26540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/12_2023/7ui6_26540.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/12_2023/7ui6_26540.pdb" } resolution = 3.7 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= 0.002 sd= 0.029 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: 5 Type Number sf(0) Gaussians Mn 4 7.51 5 S 52 5.16 5 C 6568 2.51 5 N 1736 2.21 5 O 1788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10148 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 5072 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 23, 'TRANS': 585} Chain breaks: 1 Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 5072 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 23, 'TRANS': 585} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.67, per 1000 atoms: 0.56 Number of scatterers: 10148 At special positions: 0 Unit cell: (106.6, 113.012, 113.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 4 24.99 S 52 16.00 O 1788 8.00 N 1736 7.00 C 6568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 726 " distance=2.03 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 443 " - pdb=" SG CYS B 726 " distance=2.03 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: 3.88 Conformation dependent library (CDL) restraints added in 1.7 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 8 sheets defined 48.4% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 145 through 163 removed outlier: 4.064A pdb=" N ALA A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.660A pdb=" N THR A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.606A pdb=" N LYS A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.162A pdb=" N LEU A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.020A pdb=" N LYS A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.635A pdb=" N MET A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.712A pdb=" N ASN A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.994A pdb=" N CYS A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 393 through 406 removed outlier: 3.822A pdb=" N PHE A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 427 through 435 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.695A pdb=" N PHE A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 487 through 495 Processing helix chain 'A' and resid 506 through 520 Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.962A pdb=" N MET A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.880A pdb=" N HIS A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 584 Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.524A pdb=" N GLY A 633 " --> pdb=" O TRP A 630 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 634 " --> pdb=" O THR A 631 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA A 635 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Proline residue: A 636 - end of helix No H-bonds generated for 'chain 'A' and resid 630 through 637' Processing helix chain 'A' and resid 638 through 644 removed outlier: 3.606A pdb=" N TRP A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 691 removed outlier: 3.620A pdb=" N GLN A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 removed outlier: 3.613A pdb=" N THR A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 743 removed outlier: 4.090A pdb=" N ARG A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 756 removed outlier: 3.702A pdb=" N LEU A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 163 removed outlier: 4.015A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.544A pdb=" N VAL B 208 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 250 through 257 removed outlier: 4.137A pdb=" N LEU B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 311 through 323 removed outlier: 4.024A pdb=" N MET B 315 " --> pdb=" O LYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.609A pdb=" N ASN B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.556A pdb=" N ASN B 357 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.644A pdb=" N TYR B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.940A pdb=" N VAL B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.664A pdb=" N PHE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 427 through 437 removed outlier: 3.770A pdb=" N GLU B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 451 removed outlier: 4.055A pdb=" N PHE B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.695A pdb=" N ARG B 484 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 4.431A pdb=" N ALA B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 520 Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.538A pdb=" N ARG B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 553 removed outlier: 3.829A pdb=" N HIS B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 584 removed outlier: 3.620A pdb=" N TYR B 575 " --> pdb=" O GLY B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.636A pdb=" N HIS B 634 " --> pdb=" O THR B 631 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA B 635 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Proline residue: B 636 - end of helix Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.922A pdb=" N TRP B 642 " --> pdb=" O ASN B 638 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 643' Processing helix chain 'B' and resid 680 through 691 removed outlier: 4.038A pdb=" N HIS B 684 " --> pdb=" O ASN B 680 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 720 removed outlier: 3.970A pdb=" N THR B 715 " --> pdb=" O SER B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 743 removed outlier: 3.545A pdb=" N ARG B 724 " --> pdb=" O ASN B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 756 removed outlier: 3.676A pdb=" N LEU B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS B 748 " --> pdb=" O PHE B 744 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TYR B 749 " --> pdb=" O ALA B 745 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 200 removed outlier: 6.656A pdb=" N LEU A 168 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASP A 197 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 170 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR A 199 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 172 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N HIS A 139 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU A 241 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA A 141 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 270 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLY A 298 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N GLY A 268 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU A 267 " --> pdb=" O TYR A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.783A pdb=" N ILE A 379 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 457 removed outlier: 3.528A pdb=" N ILE A 533 " --> pdb=" O HIS A 457 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE A 499 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS A 532 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 501 " --> pdb=" O HIS A 532 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 534 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 503 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N SER A 500 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A 476 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ALA A 502 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA A 478 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR A 475 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 661 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG A 664 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N LYS A 590 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A 695 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 651 " --> pdb=" O PHE A 695 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR A 649 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 597 through 599 Processing sheet with id=AA5, first strand: chain 'B' and resid 194 through 200 removed outlier: 6.674A pdb=" N HIS B 139 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU B 241 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA B 141 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL B 299 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL B 270 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 352 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU B 269 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 247 removed outlier: 3.617A pdb=" N HIS B 380 " --> pdb=" O VAL B 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 456 through 457 removed outlier: 3.555A pdb=" N ILE B 533 " --> pdb=" O HIS B 457 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 474 through 477 removed outlier: 6.093A pdb=" N THR B 475 " --> pdb=" O PHE B 560 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 661 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TYR B 660 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ARG B 664 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N LYS B 590 " --> pdb=" O ARG B 664 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA B 591 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE B 695 " --> pdb=" O VAL B 651 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1782 1.32 - 1.45: 2884 1.45 - 1.57: 5666 1.57 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 10422 Sorted by residual: bond pdb=" CA SER B 500 " pdb=" CB SER B 500 " ideal model delta sigma weight residual 1.534 1.461 0.073 1.77e-02 3.19e+03 1.72e+01 bond pdb=" N ALA B 701 " pdb=" CA ALA B 701 " ideal model delta sigma weight residual 1.454 1.500 -0.045 1.16e-02 7.43e+03 1.53e+01 bond pdb=" N GLU B 598 " pdb=" CA GLU B 598 " ideal model delta sigma weight residual 1.455 1.500 -0.044 1.18e-02 7.18e+03 1.41e+01 bond pdb=" C ALA B 502 " pdb=" N LEU B 503 " ideal model delta sigma weight residual 1.331 1.285 0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" N THR B 599 " pdb=" CA THR B 599 " ideal model delta sigma weight residual 1.454 1.499 -0.045 1.29e-02 6.01e+03 1.24e+01 ... (remaining 10417 not shown) Histogram of bond angle deviations from ideal: 96.39 - 103.95: 129 103.95 - 111.52: 4347 111.52 - 119.08: 4024 119.08 - 126.64: 5436 126.64 - 134.21: 196 Bond angle restraints: 14132 Sorted by residual: angle pdb=" N ASP A 305 " pdb=" CA ASP A 305 " pdb=" C ASP A 305 " ideal model delta sigma weight residual 111.90 102.14 9.76 1.32e+00 5.74e-01 5.46e+01 angle pdb=" N PRO B 595 " pdb=" CA PRO B 595 " pdb=" C PRO B 595 " ideal model delta sigma weight residual 110.50 121.01 -10.51 1.57e+00 4.06e-01 4.48e+01 angle pdb=" C PHE B 186 " pdb=" N GLN B 187 " pdb=" CA GLN B 187 " ideal model delta sigma weight residual 120.38 112.92 7.46 1.46e+00 4.69e-01 2.61e+01 angle pdb=" C PHE B 566 " pdb=" N LEU B 567 " pdb=" CA LEU B 567 " ideal model delta sigma weight residual 122.37 117.67 4.70 9.30e-01 1.16e+00 2.55e+01 angle pdb=" C THR B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta sigma weight residual 120.63 114.31 6.32 1.36e+00 5.41e-01 2.16e+01 ... (remaining 14127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5440 17.58 - 35.16: 589 35.16 - 52.74: 120 52.74 - 70.32: 28 70.32 - 87.90: 9 Dihedral angle restraints: 6186 sinusoidal: 2554 harmonic: 3632 Sorted by residual: dihedral pdb=" CB CYS B 443 " pdb=" SG CYS B 443 " pdb=" SG CYS B 726 " pdb=" CB CYS B 726 " ideal model delta sinusoidal sigma weight residual 93.00 163.18 -70.18 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS A 443 " pdb=" SG CYS A 443 " pdb=" SG CYS A 726 " pdb=" CB CYS A 726 " ideal model delta sinusoidal sigma weight residual 93.00 136.26 -43.26 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS A 354 " pdb=" SG CYS A 354 " pdb=" SG CYS A 369 " pdb=" CB CYS A 369 " ideal model delta sinusoidal sigma weight residual -86.00 -129.23 43.23 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 6183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1136 0.057 - 0.114: 288 0.114 - 0.170: 83 0.170 - 0.227: 13 0.227 - 0.284: 2 Chirality restraints: 1522 Sorted by residual: chirality pdb=" CA PHE B 597 " pdb=" N PHE B 597 " pdb=" C PHE B 597 " pdb=" CB PHE B 597 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CG LEU A 505 " pdb=" CB LEU A 505 " pdb=" CD1 LEU A 505 " pdb=" CD2 LEU A 505 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE B 300 " pdb=" N ILE B 300 " pdb=" C ILE B 300 " pdb=" CB ILE B 300 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1519 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 345 " -0.080 5.00e-02 4.00e+02 1.21e-01 2.36e+01 pdb=" N PRO B 346 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO B 346 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 346 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 704 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C ILE B 704 " 0.073 2.00e-02 2.50e+03 pdb=" O ILE B 704 " -0.028 2.00e-02 2.50e+03 pdb=" N HIS B 705 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 302 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C LEU A 302 " 0.067 2.00e-02 2.50e+03 pdb=" O LEU A 302 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 303 " -0.023 2.00e-02 2.50e+03 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 146 2.61 - 3.19: 9153 3.19 - 3.76: 15228 3.76 - 4.33: 21364 4.33 - 4.90: 34076 Nonbonded interactions: 79967 Sorted by model distance: nonbonded pdb=" N LYS B 608 " pdb=" OE2 GLU B 612 " model vdw 2.044 2.520 nonbonded pdb=" O LYS A 748 " pdb=" OG1 THR A 751 " model vdw 2.124 2.440 nonbonded pdb=" OD2 ASP B 244 " pdb="MN MN B 801 " model vdw 2.142 2.320 nonbonded pdb=" OD2 ASP A 671 " pdb=" NH1 ARG A 673 " model vdw 2.163 2.520 nonbonded pdb=" OD2 ASP A 244 " pdb="MN MN A 801 " model vdw 2.166 2.320 ... (remaining 79962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.010 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.920 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.170 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10422 Z= 0.297 Angle : 0.971 10.787 14132 Z= 0.546 Chirality : 0.057 0.284 1522 Planarity : 0.007 0.121 1784 Dihedral : 14.981 87.902 3822 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.79 % Favored : 94.96 % Rotamer: Outliers : 1.09 % Allowed : 2.91 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.57 (0.23), residues: 1210 helix: -0.67 (0.24), residues: 424 sheet: -2.03 (0.39), residues: 154 loop : -0.93 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP B 679 HIS 0.011 0.002 HIS B 171 PHE 0.036 0.002 PHE A 734 TYR 0.038 0.002 TYR A 702 ARG 0.056 0.001 ARG A 673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 290 time to evaluate : 1.135 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: 12 outliers final: 5 residues processed: 297 average time/residue: 0.2851 time to fit residues: 112.3768 Evaluate side-chains 274 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 269 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1029 time to fit residues: 2.5281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS A 684 HIS B 200 ASN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS B 700 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10422 Z= 0.209 Angle : 0.669 11.097 14132 Z= 0.339 Chirality : 0.044 0.204 1522 Planarity : 0.005 0.090 1784 Dihedral : 4.485 21.461 1356 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.64 % Allowed : 10.84 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1210 helix: 0.18 (0.25), residues: 438 sheet: -1.44 (0.41), residues: 140 loop : -0.66 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 679 HIS 0.012 0.001 HIS A 163 PHE 0.019 0.002 PHE B 338 TYR 0.017 0.002 TYR B 693 ARG 0.008 0.001 ARG A 673 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 271 time to evaluate : 1.291 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: 18 outliers final: 8 residues processed: 279 average time/residue: 0.2834 time to fit residues: 104.4391 Evaluate side-chains 268 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 260 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1122 time to fit residues: 3.3143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 74 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 HIS ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10422 Z= 0.196 Angle : 0.625 9.210 14132 Z= 0.316 Chirality : 0.044 0.193 1522 Planarity : 0.004 0.053 1784 Dihedral : 4.380 22.034 1356 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.18 % Allowed : 13.84 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.24), residues: 1210 helix: 0.38 (0.25), residues: 438 sheet: -1.22 (0.42), residues: 140 loop : -0.62 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 316 HIS 0.010 0.001 HIS A 163 PHE 0.027 0.002 PHE A 657 TYR 0.021 0.002 TYR A 516 ARG 0.006 0.000 ARG A 673 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 262 time to evaluate : 0.996 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: 13 outliers final: 7 residues processed: 270 average time/residue: 0.2892 time to fit residues: 102.5433 Evaluate side-chains 265 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 258 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0963 time to fit residues: 2.7416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.0870 chunk 115 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS A 684 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10422 Z= 0.214 Angle : 0.654 11.920 14132 Z= 0.326 Chirality : 0.044 0.248 1522 Planarity : 0.004 0.048 1784 Dihedral : 4.457 23.052 1356 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.91 % Allowed : 16.85 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.24), residues: 1210 helix: 0.37 (0.25), residues: 440 sheet: -1.16 (0.42), residues: 140 loop : -0.56 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 316 HIS 0.007 0.001 HIS A 163 PHE 0.015 0.002 PHE A 170 TYR 0.023 0.002 TYR B 350 ARG 0.008 0.001 ARG B 740 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 275 time to evaluate : 1.003 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: 21 outliers final: 10 residues processed: 281 average time/residue: 0.2794 time to fit residues: 103.6204 Evaluate side-chains 274 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 264 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1004 time to fit residues: 3.3808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 0.2980 chunk 29 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10422 Z= 0.190 Angle : 0.659 12.952 14132 Z= 0.323 Chirality : 0.043 0.188 1522 Planarity : 0.004 0.044 1784 Dihedral : 4.401 22.209 1356 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.82 % Allowed : 18.58 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.24), residues: 1210 helix: 0.58 (0.25), residues: 428 sheet: -0.97 (0.40), residues: 150 loop : -0.55 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 316 HIS 0.008 0.001 HIS A 163 PHE 0.015 0.001 PHE A 170 TYR 0.022 0.002 TYR B 516 ARG 0.009 0.001 ARG B 650 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 272 time to evaluate : 1.109 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: 20 outliers final: 8 residues processed: 282 average time/residue: 0.2797 time to fit residues: 105.0959 Evaluate side-chains 272 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 264 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1583 time to fit residues: 4.4243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10422 Z= 0.321 Angle : 0.753 14.368 14132 Z= 0.374 Chirality : 0.046 0.261 1522 Planarity : 0.004 0.053 1784 Dihedral : 4.917 22.660 1356 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.46 % Allowed : 18.76 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.24), residues: 1210 helix: 0.26 (0.25), residues: 436 sheet: -1.16 (0.39), residues: 164 loop : -0.60 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 189 HIS 0.008 0.001 HIS A 457 PHE 0.024 0.002 PHE A 657 TYR 0.036 0.002 TYR B 350 ARG 0.008 0.001 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 277 time to evaluate : 0.934 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: 9 residues processed: 280 average time/residue: 0.2824 time to fit residues: 104.1918 Evaluate side-chains 275 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 266 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0959 time to fit residues: 3.1373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 0.0470 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10422 Z= 0.194 Angle : 0.731 13.476 14132 Z= 0.356 Chirality : 0.045 0.254 1522 Planarity : 0.004 0.054 1784 Dihedral : 4.614 22.430 1356 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.46 % Allowed : 20.31 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.24), residues: 1210 helix: 0.37 (0.25), residues: 442 sheet: -0.88 (0.38), residues: 166 loop : -0.59 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 653 HIS 0.008 0.001 HIS B 171 PHE 0.028 0.001 PHE A 460 TYR 0.024 0.002 TYR B 516 ARG 0.008 0.001 ARG B 650 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 272 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 275 average time/residue: 0.2749 time to fit residues: 99.6382 Evaluate side-chains 280 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 271 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1145 time to fit residues: 3.3252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 69 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10422 Z= 0.216 Angle : 0.759 14.523 14132 Z= 0.368 Chirality : 0.045 0.251 1522 Planarity : 0.004 0.066 1784 Dihedral : 4.625 22.506 1356 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.00 % Allowed : 21.86 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.24), residues: 1210 helix: 0.39 (0.25), residues: 430 sheet: -1.09 (0.36), residues: 182 loop : -0.47 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 653 HIS 0.006 0.001 HIS B 171 PHE 0.024 0.001 PHE A 657 TYR 0.034 0.002 TYR B 504 ARG 0.011 0.001 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 275 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 281 average time/residue: 0.3083 time to fit residues: 115.8915 Evaluate side-chains 274 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 268 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1128 time to fit residues: 3.1321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.0470 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10422 Z= 0.257 Angle : 0.806 15.264 14132 Z= 0.391 Chirality : 0.047 0.339 1522 Planarity : 0.005 0.071 1784 Dihedral : 4.820 36.922 1356 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.64 % Allowed : 22.86 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1210 helix: 0.18 (0.25), residues: 442 sheet: -1.16 (0.36), residues: 186 loop : -0.58 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 189 HIS 0.008 0.001 HIS A 457 PHE 0.023 0.002 PHE A 657 TYR 0.046 0.002 TYR B 504 ARG 0.007 0.001 ARG B 626 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 274 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 278 average time/residue: 0.2989 time to fit residues: 108.7894 Evaluate side-chains 273 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 270 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1096 time to fit residues: 2.0445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10422 Z= 0.333 Angle : 0.878 15.518 14132 Z= 0.431 Chirality : 0.049 0.359 1522 Planarity : 0.005 0.073 1784 Dihedral : 5.241 39.549 1356 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.55 % Allowed : 23.95 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.97 (0.24), residues: 1210 helix: -0.07 (0.24), residues: 448 sheet: -1.36 (0.37), residues: 186 loop : -0.72 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 653 HIS 0.008 0.001 HIS A 457 PHE 0.027 0.002 PHE A 657 TYR 0.052 0.003 TYR B 504 ARG 0.007 0.001 ARG B 740 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 282 time to evaluate : 1.058 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: 6 outliers final: 4 residues processed: 285 average time/residue: 0.2920 time to fit residues: 109.6205 Evaluate side-chains 282 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 278 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1229 time to fit residues: 2.5277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 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 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.203210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.165855 restraints weight = 17604.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.171534 restraints weight = 10123.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.175586 restraints weight = 6892.822| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10422 Z= 0.245 Angle : 0.840 14.963 14132 Z= 0.410 Chirality : 0.048 0.327 1522 Planarity : 0.005 0.072 1784 Dihedral : 5.067 40.452 1356 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.27 % Allowed : 25.50 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.92 (0.24), residues: 1210 helix: 0.02 (0.24), residues: 448 sheet: -1.31 (0.36), residues: 184 loop : -0.76 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 653 HIS 0.008 0.001 HIS B 171 PHE 0.024 0.002 PHE A 657 TYR 0.051 0.002 TYR B 504 ARG 0.010 0.001 ARG B 626 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2685.78 seconds wall clock time: 49 minutes 11.87 seconds (2951.87 seconds total)