Starting phenix.real_space_refine (version: dev) on Tue Dec 13 00:20:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/12_2022/7b1b_11982.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/12_2022/7b1b_11982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/12_2022/7b1b_11982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/12_2022/7b1b_11982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/12_2022/7b1b_11982.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/12_2022/7b1b_11982.pdb" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "B GLU 530": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 12870 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5484 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PTRANS': 33, 'TRANS': 720} Unresolved non-hydrogen bonds: 564 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 21, 'ASN:plan1': 13, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 369 Chain: "D" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 747 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 93} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "P" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 680 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 86} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 5666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5666 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 33, 'TRANS': 718} Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 280 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 16, 'ASN:plan1': 12, 'HIS:plan': 4, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 256 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.49, per 1000 atoms: 0.58 Number of scatterers: 12870 At special positions: 0 Unit cell: (101.26, 133.63, 164.34, 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 69 16.00 O 2498 8.00 N 2141 7.00 C 8162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 46 " distance=2.02 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 57 " distance=2.04 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 561 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 622 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 783 " distance=2.03 Simple disulfide: pdb=" SG CYS D 10 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS P 59 " distance=2.03 Simple disulfide: pdb=" SG CYS D 94 " - pdb=" SG CYS P 94 " distance=2.03 Simple disulfide: pdb=" SG CYS P 10 " - pdb=" SG CYS P 65 " distance=2.03 Simple disulfide: pdb=" SG CYS P 47 " - pdb=" SG CYS P 95 " distance=2.02 Simple disulfide: pdb=" SG CYS P 56 " - pdb=" SG CYS P 97 " distance=2.02 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 104 " distance=2.04 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 561 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 767 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 783 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 801 " - " ASN A 481 " " NAG A 802 " - " ASN A 521 " " NAG A 803 " - " ASN A 687 " " NAG C 1 " - " ASN A 634 " " NAG E 1 " - " ASN A 151 " " NAG G 1 " - " ASN A 194 " " NAG H 1 " - " ASN B 194 " " NAG I 1 " - " ASN B 151 " " NAG J 1 " - " ASN B 481 " " NAG K 1 " - " ASN B 521 " Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 1.8 seconds 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3288 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 21 sheets defined 11.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.593A pdb=" N TYR A 142 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.528A pdb=" N SER A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 168' Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.817A pdb=" N ALA A 191 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.763A pdb=" N LEU A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.591A pdb=" N PHE A 453 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 563 through 571 Processing helix chain 'A' and resid 602 through 606 Processing helix chain 'A' and resid 672 through 676 removed outlier: 3.714A pdb=" N LYS A 676 " --> pdb=" O ASN A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 723 removed outlier: 4.195A pdb=" N ALA A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 756 through 759 Processing helix chain 'A' and resid 761 through 765 Processing helix chain 'D' and resid 25 through 29 removed outlier: 4.070A pdb=" N MET D 29 " --> pdb=" O ASN D 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.524A pdb=" N SER B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 removed outlier: 4.141A pdb=" N PHE B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B 263 " --> pdb=" O ASN B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.508A pdb=" N ALA B 405 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 407 " --> pdb=" O LYS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 removed outlier: 3.593A pdb=" N VAL B 470 " --> pdb=" O PRO B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.706A pdb=" N TRP B 491 " --> pdb=" O PHE B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 563 through 571 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 716 through 723 removed outlier: 3.978A pdb=" N LEU B 720 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.263A pdb=" N ILE B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 755 " --> pdb=" O PHE B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 777 Processing helix chain 'B' and resid 778 through 783 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.627A pdb=" N TYR A 56 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 68 removed outlier: 6.338A pdb=" N VAL A 74 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A 102 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE A 76 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 201 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 247 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 297 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 320 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 7.337A pdb=" N ILE A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.723A pdb=" N LEU A 367 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU A 391 " --> pdb=" O HIS A 416 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU A 415 " --> pdb=" O TYR A 440 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 439 " --> pdb=" O HIS A 478 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 477 " --> pdb=" O ASP A 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 526 through 527 removed outlier: 6.216A pdb=" N LEU A 526 " --> pdb=" O ASN A 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 548 through 549 removed outlier: 6.741A pdb=" N ILE A 548 " --> pdb=" O GLN A 579 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 620 through 625 removed outlier: 3.573A pdb=" N GLU A 660 " --> pdb=" O VAL A 631 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 682 through 683 Processing sheet with id=AA9, first strand: chain 'D' and resid 13 through 17 Processing sheet with id=AB1, first strand: chain 'D' and resid 65 through 68 Processing sheet with id=AB2, first strand: chain 'D' and resid 87 through 89 removed outlier: 6.621A pdb=" N GLU D 87 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 12 through 15 Processing sheet with id=AB4, first strand: chain 'P' and resid 66 through 70 removed outlier: 5.796A pdb=" N LYS P 66 " --> pdb=" O CYS P 95 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS P 95 " --> pdb=" O LYS P 66 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU P 68 " --> pdb=" O SER P 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AB7, first strand: chain 'B' and resid 151 through 154 removed outlier: 6.389A pdb=" N LEU B 175 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 245 through 248 removed outlier: 6.423A pdb=" N VAL B 319 " --> pdb=" O ASN B 344 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 367 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 392 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 438 through 439 removed outlier: 3.730A pdb=" N HIS B 478 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 502 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 510 through 512 removed outlier: 6.880A pdb=" N LEU B 511 " --> pdb=" O LEU B 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 631 through 634 Processing sheet with id=AC3, first strand: chain 'B' and resid 682 through 683 160 hydrogen bonds defined for protein. 375 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: 4.25 Time building geometry restraints manager: 6.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4256 1.34 - 1.47: 2868 1.47 - 1.59: 5889 1.59 - 1.71: 0 1.71 - 1.83: 86 Bond restraints: 13099 Sorted by residual: bond pdb=" C SER B 332 " pdb=" N LEU B 333 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.40e-02 5.10e+03 3.20e+00 bond pdb=" CA TYR A 79 " pdb=" C TYR A 79 " ideal model delta sigma weight residual 1.522 1.492 0.029 1.72e-02 3.38e+03 2.89e+00 bond pdb=" CA ASN B 444 " pdb=" CB ASN B 444 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.62e-02 3.81e+03 2.39e+00 bond pdb=" CG1 ILE A 522 " pdb=" CD1 ILE A 522 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.27e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.426 1.469 -0.043 3.20e-02 9.77e+02 1.84e+00 ... (remaining 13094 not shown) Histogram of bond angle deviations from ideal: 96.38 - 103.92: 173 103.92 - 111.47: 6187 111.47 - 119.01: 4665 119.01 - 126.55: 6731 126.55 - 134.09: 131 Bond angle restraints: 17887 Sorted by residual: angle pdb=" O LEU B 446 " pdb=" C LEU B 446 " pdb=" N ALA B 447 " ideal model delta sigma weight residual 122.75 103.10 19.65 1.16e+00 7.43e-01 2.87e+02 angle pdb=" C GLN B 442 " pdb=" CA GLN B 442 " pdb=" CB GLN B 442 " ideal model delta sigma weight residual 115.89 108.61 7.28 1.32e+00 5.74e-01 3.04e+01 angle pdb=" N VAL B 74 " pdb=" CA VAL B 74 " pdb=" C VAL B 74 " ideal model delta sigma weight residual 112.43 108.16 4.27 9.20e-01 1.18e+00 2.15e+01 angle pdb=" C2 NAG I 2 " pdb=" N2 NAG I 2 " pdb=" C7 NAG I 2 " ideal model delta sigma weight residual 123.12 128.98 -5.86 1.28e+00 6.08e-01 2.09e+01 angle pdb=" N VAL P 75 " pdb=" CA VAL P 75 " pdb=" C VAL P 75 " ideal model delta sigma weight residual 113.20 109.05 4.15 9.60e-01 1.09e+00 1.87e+01 ... (remaining 17882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.03: 7313 21.03 - 42.05: 619 42.05 - 63.08: 65 63.08 - 84.10: 4 84.10 - 105.13: 3 Dihedral angle restraints: 8004 sinusoidal: 2983 harmonic: 5021 Sorted by residual: dihedral pdb=" CB CYS B 35 " pdb=" SG CYS B 35 " pdb=" SG CYS B 46 " pdb=" CB CYS B 46 " ideal model delta sinusoidal sigma weight residual 93.00 13.14 79.86 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS B 616 " pdb=" SG CYS B 616 " pdb=" SG CYS B 622 " pdb=" CB CYS B 622 " ideal model delta sinusoidal sigma weight residual -86.00 -14.35 -71.65 1 1.00e+01 1.00e-02 6.58e+01 dihedral pdb=" CB CYS B 561 " pdb=" SG CYS B 561 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual 93.00 146.73 -53.73 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 8001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1919 0.062 - 0.124: 291 0.124 - 0.186: 14 0.186 - 0.248: 1 0.248 - 0.310: 1 Chirality restraints: 2226 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 151 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.14e+00 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 521 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2223 not shown) Planarity restraints: 2313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 446 " 0.086 2.00e-02 2.50e+03 1.54e-01 2.37e+02 pdb=" C LEU B 446 " -0.266 2.00e-02 2.50e+03 pdb=" O LEU B 446 " 0.097 2.00e-02 2.50e+03 pdb=" N ALA B 447 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 624 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C MET B 624 " -0.031 2.00e-02 2.50e+03 pdb=" O MET B 624 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG B 625 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 76 " 0.016 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE B 76 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 76 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 76 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 76 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 76 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 76 " 0.005 2.00e-02 2.50e+03 ... (remaining 2310 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 451 2.65 - 3.21: 14565 3.21 - 3.77: 22646 3.77 - 4.34: 30374 4.34 - 4.90: 45189 Nonbonded interactions: 113225 Sorted by model distance: nonbonded pdb=" OG SER B 708 " pdb=" O ARG B 733 " model vdw 2.087 2.440 nonbonded pdb=" OG1 THR B 466 " pdb=" OD2 ASP B 490 " model vdw 2.118 2.440 nonbonded pdb=" O GLU A 418 " pdb=" ND2 ASN A 420 " model vdw 2.143 2.520 nonbonded pdb=" O HIS D 70 " pdb=" NH1 ARG D 72 " model vdw 2.145 2.520 nonbonded pdb=" OG SER A 504 " pdb=" ND2 ASN A 525 " model vdw 2.158 2.520 ... (remaining 113220 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' and (resid 32 through 37 or (resid 38 through 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 46 or (resid 47 through \ 48 and (name N or name CA or name C or name O or name CB )) or resid 49 through \ 50 or (resid 51 through 53 and (name N or name CA or name C or name O or name C \ B )) or resid 54 through 58 or (resid 59 and (name N or name CA or name C or nam \ e O or name CB )) or resid 60 or (resid 61 and (name N or name CA or name C or n \ ame O or name CB )) or resid 62 through 66 or (resid 67 and (name N or name CA o \ r name C or name O or name CB )) or resid 68 or (resid 69 through 72 and (name N \ or name CA or name C or name O or name CB )) or resid 73 through 79 or (resid 8 \ 0 through 81 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 2 through 157 or (resid 158 and (name N or name CA or name C or name O or name C \ B )) or resid 159 through 406 or (resid 407 and (name N or name CA or name C or \ name O or name CB )) or resid 408 through 450 or (resid 451 and (name N or name \ CA or name C or name O or name CB )) or resid 452 through 454 or (resid 455 and \ (name N or name CA or name C or name O or name CB )) or resid 456 or (resid 457 \ and (name N or name CA or name C or name O or name CB )) or resid 458 or (resid \ 459 and (name N or name CA or name C or name O or name CB )) or resid 460 throug \ h 461 or (resid 462 through 465 and (name N or name CA or name C or name O or na \ me CB )) or resid 466 through 469 or (resid 470 through 473 and (name N or name \ CA or name C or name O or name CB )) or resid 474 through 644 or (resid 645 thro \ ugh 646 and (name N or name CA or name C or name O or name CB )) or resid 647 th \ rough 664 or (resid 665 and (name N or name CA or name C or name O or name CB )) \ or resid 666 through 675 or (resid 676 and (name N or name CA or name C or name \ O or name CB )) or resid 677 through 708 or (resid 709 and (name N or name CA o \ r name C or name O or name CB )) or resid 710 through 783)) selection = (chain 'B' and (resid 32 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 62 or (resid 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 74 or (resid 75 and ( \ name N or name CA or name C or name O or name CB )) or resid 76 through 83 or (r \ esid 84 through 88 and (name N or name CA or name C or name O or name CB )) or r \ esid 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) or \ resid 91 through 92 or (resid 93 and (name N or name CA or name C or name O or \ name CB )) or resid 94 or (resid 95 through 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 through 102 or (resid 103 and (name N or nam \ e CA or name C or name O or name CB )) or resid 104 through 116 or (resid 117 an \ d (name N or name CA or name C or name O or name CB )) or resid 118 through 122 \ or (resid 123 and (name N or name CA or name C or name O or name CB )) or resid \ 124 through 132 or (resid 133 and (name N or name CA or name C or name O or name \ CB )) or resid 134 through 136 or (resid 137 and (name N or name CA or name C o \ r name O or name CB )) or resid 138 through 145 or (resid 146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 147 or (resid 148 and (name N or \ name CA or name C or name O or name CB )) or resid 149 through 160 or (resid 16 \ 1 through 166 and (name N or name CA or name C or name O or name CB )) or resid \ 167 through 172 or (resid 173 and (name N or name CA or name C or name O or name \ CB )) or resid 174 through 177 or (resid 178 and (name N or name CA or name C o \ r name O or name CB )) or resid 179 through 180 or (resid 181 and (name N or nam \ e CA or name C or name O or name CB )) or resid 182 through 184 or (resid 185 an \ d (name N or name CA or name C or name O or name CB )) or resid 186 through 205 \ or (resid 206 through 209 and (name N or name CA or name C or name O or name CB \ )) or resid 210 through 211 or (resid 212 through 213 and (name N or name CA or \ name C or name O or name CB )) or resid 214 through 216 or (resid 217 through 21 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 219 or (resi \ d 220 through 221 and (name N or name CA or name C or name O or name CB )) or re \ sid 222 through 227 or (resid 228 and (name N or name CA or name C or name O or \ name CB )) or resid 229 or (resid 230 and (name N or name CA or name C or name O \ or name CB )) or resid 231 through 232 or (resid 233 through 234 and (name N or \ name CA or name C or name O or name CB )) or resid 235 or (resid 236 and (name \ N or name CA or name C or name O or name CB )) or resid 237 through 240 or (resi \ d 241 through 245 and (name N or name CA or name C or name O or name CB )) or re \ sid 246 through 248 or (resid 249 and (name N or name CA or name C or name O or \ name CB )) or resid 250 through 251 or (resid 252 and (name N or name CA or name \ C or name O or name CB )) or resid 253 or (resid 254 through 255 and (name N or \ name CA or name C or name O or name CB )) or resid 256 or (resid 257 through 25 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 264 or (resid 265 through 266 and (name N or name CA or name C or name O or name \ CB )) or resid 267 through 268 or (resid 269 and (name N or name CA or name C o \ r name O or name CB )) or resid 270 through 278 or (resid 279 and (name N or nam \ e CA or name C or name O or name CB )) or resid 280 through 281 or (resid 282 an \ d (name N or name CA or name C or name O or name CB )) or resid 283 through 285 \ or (resid 286 through 290 and (name N or name CA or name C or name O or name CB \ )) or resid 291 through 306 or (resid 307 and (name N or name CA or name C or na \ me O or name CB )) or resid 308 through 420 or (resid 421 and (name N or name CA \ or name C or name O or name CB )) or resid 422 through 443 or (resid 444 and (n \ ame N or name CA or name C or name O or name CB )) or resid 445 through 453 or ( \ resid 454 through 455 and (name N or name CA or name C or name O or name CB )) o \ r resid 456 through 559 or (resid 560 and (name N or name CA or name C or name O \ or name CB )) or resid 561 through 608 or (resid 609 and (name N or name CA or \ name C or name O or name CB )) or resid 610 or (resid 611 through 615 and (name \ N or name CA or name C or name O or name CB )) or resid 616 through 641 or (resi \ d 642 and (name N or name CA or name C or name O or name CB )) or resid 643 thro \ ugh 651 or (resid 652 through 655 and (name N or name CA or name C or name O or \ name CB )) or resid 656 or (resid 657 through 658 and (name N or name CA or name \ C or name O or name CB )) or resid 659 through 669 or (resid 670 and (name N or \ name CA or name C or name O or name CB )) or resid 671 through 693 or (resid 69 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 695 or (resi \ d 696 and (name N or name CA or name C or name O or name CB )) or resid 697 thro \ ugh 712 or (resid 713 and (name N or name CA or name C or name O or name CB )) o \ r resid 714 through 722 or (resid 723 through 725 and (name N or name CA or name \ C or name O or name CB )) or resid 726 through 764 or (resid 765 through 766 an \ d (name N or name CA or name C or name O or name CB )) or resid 767 through 769 \ or (resid 770 and (name N or name CA or name C or name O or name CB )) or (resid \ 771 through 773 and (name N or name CA or name C or name O or name CB )) or res \ id 774 or (resid 775 and (name N or name CA or name C or name O or name CB )) or \ resid 776 through 783)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = (chain 'D' and (resid 6 through 19 or (resid 20 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 34 or (resid 35 through \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 through \ 49 or (resid 50 through 52 and (name N or name CA or name C or name O or name CB \ )) or resid 53 or (resid 54 and (name N or name CA or name C or name O or name \ CB )) or resid 55 through 59 or (resid 60 through 61 and (name N or name CA or n \ ame C or name O or name CB )) or resid 62 or (resid 63 and (name N or name CA or \ name C or name O or name CB )) or resid 64 through 82 or (resid 83 and (name N \ or name CA or name C or name O or name CB )) or resid 84 through 85 or (resid 86 \ through 88 and (name N or name CA or name C or name O or name CB )) or resid 89 \ through 97)) selection = (chain 'P' and (resid 6 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 23 or (resid 24 through 28 and (nam \ e N or name CA or name C or name O or name CB )) or resid 29 through 38 or (resi \ d 39 through 40 and (name N or name CA or name C or name O or name CB )) or resi \ d 41 through 79 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 97)) } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 8162 2.51 5 N 2141 2.21 5 O 2498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.060 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: 0.000 Extract box with map and model: 11.760 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.100 Process input model: 36.210 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 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 : 0.004 0.059 13099 Z= 0.263 Angle : 0.699 19.649 17887 Z= 0.378 Chirality : 0.043 0.310 2226 Planarity : 0.005 0.154 2303 Dihedral : 14.148 105.129 4638 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 33.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer Outliers : 0.54 % 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: -2.84 (0.20), residues: 1689 helix: -1.34 (0.58), residues: 87 sheet: -1.87 (0.33), residues: 254 loop : -2.11 (0.16), residues: 1348 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 1.783 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 28 average time/residue: 0.2005 time to fit residues: 10.9142 Evaluate side-chains 23 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 1.699 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1113 time to fit residues: 2.4232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.3980 chunk 127 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 13099 Z= 0.270 Angle : 0.688 10.781 17887 Z= 0.356 Chirality : 0.045 0.300 2226 Planarity : 0.004 0.059 2303 Dihedral : 6.616 105.516 1924 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 30.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.09 % Favored : 85.91 % Rotamer Outliers : 0.08 % 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: -2.82 (0.20), residues: 1689 helix: -1.54 (0.51), residues: 100 sheet: -1.70 (0.33), residues: 261 loop : -2.12 (0.17), residues: 1328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 1.609 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.2057 time to fit residues: 9.5227 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 42 optimal weight: 40.0000 chunk 152 optimal weight: 30.0000 chunk 165 optimal weight: 20.0000 chunk 136 optimal weight: 0.6980 chunk 151 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 122 optimal weight: 0.1980 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 13099 Z= 0.203 Angle : 0.621 10.260 17887 Z= 0.320 Chirality : 0.044 0.299 2226 Planarity : 0.004 0.073 2303 Dihedral : 6.409 105.180 1924 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer Outliers : 0.00 % 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: -2.78 (0.20), residues: 1689 helix: -1.64 (0.49), residues: 100 sheet: -1.60 (0.32), residues: 275 loop : -2.09 (0.17), residues: 1314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2112 time to fit residues: 9.5340 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.727 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 30.0000 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 396 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 13099 Z= 0.294 Angle : 0.676 11.178 17887 Z= 0.344 Chirality : 0.044 0.289 2226 Planarity : 0.004 0.054 2303 Dihedral : 6.598 105.395 1924 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 30.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.56 % Favored : 86.44 % Rotamer Outliers : 0.08 % 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: -2.89 (0.20), residues: 1689 helix: -1.34 (0.47), residues: 111 sheet: -1.90 (0.32), residues: 272 loop : -2.15 (0.17), residues: 1306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.2100 time to fit residues: 9.7984 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 HIS ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 13099 Z= 0.365 Angle : 0.737 10.427 17887 Z= 0.374 Chirality : 0.045 0.303 2226 Planarity : 0.005 0.057 2303 Dihedral : 6.869 105.811 1924 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 35.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Rotamer Outliers : 0.00 % 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: -3.00 (0.20), residues: 1689 helix: -1.63 (0.48), residues: 111 sheet: -1.95 (0.32), residues: 263 loop : -2.21 (0.17), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2193 time to fit residues: 9.9765 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 30.0000 chunk 146 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 13 optimal weight: 40.0000 chunk 53 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 13099 Z= 0.308 Angle : 0.688 11.670 17887 Z= 0.352 Chirality : 0.044 0.301 2226 Planarity : 0.004 0.047 2303 Dihedral : 6.822 105.910 1924 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 33.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.45 % Favored : 85.49 % Rotamer Outliers : 0.00 % 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: -2.98 (0.20), residues: 1689 helix: -1.59 (0.48), residues: 111 sheet: -1.94 (0.32), residues: 263 loop : -2.20 (0.17), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2093 time to fit residues: 9.6554 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 161 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 74 optimal weight: 0.0770 overall best weight: 6.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 GLN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 13099 Z= 0.331 Angle : 0.717 10.970 17887 Z= 0.364 Chirality : 0.045 0.299 2226 Planarity : 0.004 0.045 2303 Dihedral : 6.928 105.845 1924 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 34.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.68 % Favored : 85.26 % Rotamer Outliers : 0.00 % 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: -3.03 (0.20), residues: 1689 helix: -1.74 (0.49), residues: 106 sheet: -1.99 (0.32), residues: 266 loop : -2.22 (0.17), residues: 1317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2129 time to fit residues: 9.6028 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 102 optimal weight: 30.0000 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 HIS ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 13099 Z= 0.325 Angle : 0.714 10.765 17887 Z= 0.363 Chirality : 0.045 0.302 2226 Planarity : 0.004 0.048 2303 Dihedral : 6.981 105.789 1924 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 34.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.04 % Favored : 84.90 % Rotamer Outliers : 0.00 % 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: -3.04 (0.20), residues: 1689 helix: -1.60 (0.48), residues: 111 sheet: -2.06 (0.32), residues: 266 loop : -2.23 (0.17), residues: 1312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2055 time to fit residues: 9.1511 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 159 optimal weight: 0.0470 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 13099 Z= 0.208 Angle : 0.634 10.636 17887 Z= 0.324 Chirality : 0.044 0.299 2226 Planarity : 0.004 0.050 2303 Dihedral : 6.678 105.386 1924 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 27.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.20 % Favored : 86.74 % Rotamer Outliers : 0.00 % 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: -2.84 (0.20), residues: 1689 helix: -1.54 (0.48), residues: 111 sheet: -1.73 (0.33), residues: 257 loop : -2.13 (0.17), residues: 1321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2192 time to fit residues: 9.8241 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 102 optimal weight: 40.0000 chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 13099 Z= 0.199 Angle : 0.619 10.344 17887 Z= 0.315 Chirality : 0.043 0.289 2226 Planarity : 0.004 0.077 2303 Dihedral : 6.525 105.355 1924 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer Outliers : 0.00 % 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: -2.79 (0.20), residues: 1689 helix: -1.43 (0.49), residues: 111 sheet: -1.66 (0.32), residues: 269 loop : -2.10 (0.17), residues: 1309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2286 time to fit residues: 10.1376 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 137 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.025503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.018979 restraints weight = 262035.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.019443 restraints weight = 183311.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.019770 restraints weight = 141508.523| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 13099 Z= 0.180 Angle : 0.602 12.561 17887 Z= 0.306 Chirality : 0.043 0.282 2226 Planarity : 0.004 0.047 2303 Dihedral : 6.326 105.111 1924 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer Outliers : 0.00 % 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: -2.71 (0.20), residues: 1689 helix: -1.38 (0.49), residues: 111 sheet: -1.52 (0.33), residues: 264 loop : -2.07 (0.17), residues: 1314 =============================================================================== Job complete usr+sys time: 1921.10 seconds wall clock time: 36 minutes 47.10 seconds (2207.10 seconds total)