Starting phenix.real_space_refine on Sun Dec 10 00:57:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/12_2023/7b1b_11982.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/12_2023/7b1b_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_2023/7b1b_11982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/12_2023/7b1b_11982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/12_2023/7b1b_11982.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/12_2023/7b1b_11982.pdb" } resolution = 4.23 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= 0.001 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6 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: 6 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: 6 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 dihedrals: 6 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: 6 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 dihedrals: 6 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: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.34, per 1000 atoms: 0.57 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: 5.87 Conformation dependent library (CDL) restraints added in 2.3 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: 1.50 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: 4.00 Time building geometry restraints manager: 6.30 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=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.00e+01 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=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+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 ... (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=" 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 angle pdb=" N GLU A 308 " pdb=" CA GLU A 308 " pdb=" CB GLU A 308 " ideal model delta sigma weight residual 113.65 108.63 5.02 1.47e+00 4.63e-01 1.17e+01 ... (remaining 17882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 7634 23.85 - 47.70: 511 47.70 - 71.54: 58 71.54 - 95.39: 3 95.39 - 119.24: 3 Dihedral angle restraints: 8209 sinusoidal: 3188 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 8206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1895 0.062 - 0.124: 304 0.124 - 0.186: 20 0.186 - 0.248: 1 0.248 - 0.310: 6 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=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.97e+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 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: 5.340 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: 12.380 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.450 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.100 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 0.063 13099 Z= 0.289 Angle : 0.752 19.649 17887 Z= 0.384 Chirality : 0.046 0.310 2226 Planarity : 0.005 0.154 2303 Dihedral : 14.668 119.239 4843 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 33.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 0.54 % Allowed : 27.91 % Favored : 71.55 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 31 HIS 0.007 0.001 HIS A 132 PHE 0.029 0.001 PHE B 76 TYR 0.014 0.002 TYR B 129 ARG 0.003 0.001 ARG A 349 *********************** 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 : 1.520 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 28 average time/residue: 0.2050 time to fit residues: 11.2287 Evaluate side-chains 23 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 1.677 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1331 time to fit residues: 2.5178 ------------------------------------------------------------------------------- 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 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** D 88 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13099 Z= 0.265 Angle : 0.707 10.800 17887 Z= 0.353 Chirality : 0.046 0.234 2226 Planarity : 0.004 0.061 2303 Dihedral : 9.229 113.105 2129 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 30.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % Rotamer: Outliers : 0.08 % Allowed : 6.06 % Favored : 93.87 % 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: -2.85 (0.20), residues: 1689 helix: -1.54 (0.51), residues: 100 sheet: -1.81 (0.32), residues: 277 loop : -2.11 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 31 HIS 0.008 0.002 HIS B 416 PHE 0.022 0.002 PHE B 76 TYR 0.025 0.002 TYR A 684 ARG 0.003 0.001 ARG A 475 *********************** 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 : 1.481 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.2045 time to fit residues: 9.4769 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: 2.0246 ------------------------------------------------------------------------------- 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: 6.9990 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: 0.9980 chunk 165 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 122 optimal weight: 0.1980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13099 Z= 0.176 Angle : 0.631 10.323 17887 Z= 0.312 Chirality : 0.044 0.234 2226 Planarity : 0.004 0.071 2303 Dihedral : 8.687 112.113 2129 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 24.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % 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: -2.74 (0.20), residues: 1689 helix: -1.50 (0.49), residues: 105 sheet: -1.58 (0.32), residues: 275 loop : -2.07 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 31 HIS 0.007 0.001 HIS A 478 PHE 0.025 0.001 PHE B 381 TYR 0.022 0.001 TYR A 684 ARG 0.008 0.000 ARG B 125 *********************** 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 : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2098 time to fit residues: 9.3489 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0722 ------------------------------------------------------------------------------- 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: 20.0000 chunk 79 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 102 optimal weight: 30.0000 chunk 153 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 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 373 GLN B 396 ASN B 554 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 13099 Z= 0.411 Angle : 0.836 11.801 17887 Z= 0.408 Chirality : 0.047 0.283 2226 Planarity : 0.005 0.049 2303 Dihedral : 9.140 114.706 2129 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 41.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.22 % Favored : 84.78 % Rotamer: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % 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 (0.46), residues: 117 sheet: -1.96 (0.32), residues: 263 loop : -2.25 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP P 31 HIS 0.014 0.002 HIS A 478 PHE 0.020 0.002 PHE B 118 TYR 0.024 0.003 TYR B 684 ARG 0.009 0.001 ARG A 475 *********************** 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 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2107 time to fit residues: 9.3616 Evaluate side-chains 21 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0097 ------------------------------------------------------------------------------- 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: 6.9990 chunk 92 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 0.0770 chunk 145 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- 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 688 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** ** 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: 0.8449 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13099 Z= 0.256 Angle : 0.678 10.570 17887 Z= 0.336 Chirality : 0.045 0.234 2226 Planarity : 0.004 0.057 2303 Dihedral : 8.739 113.415 2129 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 31.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -2.96 (0.20), residues: 1689 helix: -1.61 (0.48), residues: 111 sheet: -1.92 (0.32), residues: 273 loop : -2.18 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 31 HIS 0.008 0.002 HIS A 478 PHE 0.020 0.002 PHE A 610 TYR 0.017 0.002 TYR A 684 ARG 0.005 0.001 ARG A 475 *********************** 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 23 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2071 time to fit residues: 9.6011 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.448 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0467 ------------------------------------------------------------------------------- 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: 9.9990 chunk 32 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 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: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** 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 ** 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: 0.8496 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 13099 Z= 0.423 Angle : 0.833 12.704 17887 Z= 0.407 Chirality : 0.046 0.260 2226 Planarity : 0.005 0.057 2303 Dihedral : 9.113 114.238 2129 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 41.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.81 % Favored : 84.13 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: -3.16 (0.20), residues: 1689 helix: -1.69 (0.48), residues: 112 sheet: -2.13 (0.32), residues: 266 loop : -2.31 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP P 31 HIS 0.012 0.002 HIS A 478 PHE 0.019 0.002 PHE B 118 TYR 0.022 0.003 TYR B 684 ARG 0.008 0.001 ARG A 475 *********************** 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 : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2155 time to fit residues: 9.7898 Evaluate side-chains 21 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 1.428 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1327 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 469 GLN ** 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13099 Z= 0.189 Angle : 0.654 11.316 17887 Z= 0.323 Chirality : 0.044 0.232 2226 Planarity : 0.004 0.053 2303 Dihedral : 8.514 111.967 2129 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -2.85 (0.20), residues: 1689 helix: -1.72 (0.49), residues: 106 sheet: -1.66 (0.33), residues: 257 loop : -2.13 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 31 HIS 0.006 0.001 HIS A 132 PHE 0.019 0.001 PHE B 76 TYR 0.015 0.001 TYR A 684 ARG 0.003 0.001 ARG B 282 *********************** 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 : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2591 time to fit residues: 10.8679 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1973 ------------------------------------------------------------------------------- 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: 7.9990 chunk 96 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN 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** ** 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: 0.8428 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13099 Z= 0.186 Angle : 0.634 11.221 17887 Z= 0.311 Chirality : 0.044 0.275 2226 Planarity : 0.004 0.049 2303 Dihedral : 8.260 111.378 2129 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -2.80 (0.20), residues: 1689 helix: -1.65 (0.47), residues: 117 sheet: -1.62 (0.32), residues: 276 loop : -2.10 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 31 HIS 0.006 0.001 HIS A 132 PHE 0.017 0.001 PHE B 76 TYR 0.016 0.001 TYR A 684 ARG 0.004 0.000 ARG A 475 *********************** 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 : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2062 time to fit residues: 9.2858 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.555 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0687 ------------------------------------------------------------------------------- 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: 2.9990 chunk 141 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 99 optimal weight: 0.0980 chunk 159 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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** ** 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: 0.8420 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13099 Z= 0.178 Angle : 0.618 10.794 17887 Z= 0.303 Chirality : 0.044 0.307 2226 Planarity : 0.004 0.047 2303 Dihedral : 8.088 110.483 2129 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -2.72 (0.20), residues: 1689 helix: -1.36 (0.49), residues: 111 sheet: -1.66 (0.31), residues: 284 loop : -2.03 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 31 HIS 0.006 0.001 HIS A 132 PHE 0.018 0.001 PHE B 76 TYR 0.015 0.001 TYR A 684 ARG 0.004 0.000 ARG B 125 *********************** 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 : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2150 time to fit residues: 9.5044 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0513 ------------------------------------------------------------------------------- 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: 7.9990 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 167 optimal weight: 30.0000 chunk 154 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 102 optimal weight: 40.0000 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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** ** 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: 0.8434 moved from start: 0.2450 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= 0.212 Angle : 0.631 10.693 17887 Z= 0.309 Chirality : 0.043 0.275 2226 Planarity : 0.004 0.045 2303 Dihedral : 8.136 111.505 2129 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -1.20 (0.52), residues: 105 sheet: -1.84 (0.30), residues: 301 loop : -1.99 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 31 HIS 0.006 0.001 HIS A 132 PHE 0.015 0.001 PHE B 76 TYR 0.015 0.002 TYR A 684 ARG 0.004 0.001 ARG A 475 ********************** 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 : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2109 time to fit residues: 9.5209 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1292 ------------------------------------------------------------------------------- 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: 20.0000 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 137 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.025467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.018930 restraints weight = 262301.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.019389 restraints weight = 182011.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.019727 restraints weight = 141076.357| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13099 Z= 0.190 Angle : 0.621 10.676 17887 Z= 0.304 Chirality : 0.043 0.264 2226 Planarity : 0.004 0.045 2303 Dihedral : 8.074 111.225 2129 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -2.70 (0.20), residues: 1689 helix: -1.33 (0.50), residues: 111 sheet: -1.63 (0.31), residues: 279 loop : -2.04 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 31 HIS 0.006 0.001 HIS A 132 PHE 0.016 0.001 PHE B 76 TYR 0.015 0.001 TYR A 684 ARG 0.005 0.001 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.78 seconds wall clock time: 39 minutes 53.30 seconds (2393.30 seconds total)