Starting phenix.real_space_refine on Mon Nov 18 15:18:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/11_2024/7xsq_33431.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/11_2024/7xsq_33431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/11_2024/7xsq_33431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/11_2024/7xsq_33431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/11_2024/7xsq_33431.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsq_33431/11_2024/7xsq_33431.cif" } resolution = 2.88 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= 0.003 sd= 0.043 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 34 5.49 5 S 58 5.16 5 C 10416 2.51 5 N 2871 2.21 5 O 3190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 151 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16573 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1289, 10360 Classifications: {'peptide': 1289} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1228} Chain breaks: 4 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 5497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5497 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 20, 'TRANS': 657} Chain breaks: 1 Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 4, 'rna3p_pyr': 12} Link IDs: {'rna2p': 18, 'rna3p': 15} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 676 SG CYS A 88 73.809 53.222 16.483 1.00 45.82 S ATOM 947 SG CYS A 121 76.522 51.899 14.048 1.00 61.32 S ATOM 993 SG CYS A 127 76.225 56.086 15.747 1.00 45.94 S ATOM 1017 SG CYS A 130 77.046 53.458 18.103 1.00 42.70 S ATOM 3719 SG CYS A 491 52.437 61.408 42.912 1.00 46.51 S ATOM 3787 SG CYS A 501 53.083 59.323 39.953 1.00 44.14 S ATOM 3801 SG CYS A 503 51.299 62.610 39.196 1.00 43.50 S ATOM 3823 SG CYS A 506 54.777 63.351 39.866 1.00 41.76 S ATOM 5794 SG CYS A 750 39.273 68.362 70.149 1.00 58.43 S ATOM 5807 SG CYS A 752 37.664 71.672 69.253 1.00 50.96 S ATOM 5829 SG CYS A 755 41.156 71.793 68.251 1.00 44.65 S ATOM 7828 SG CYS A1018 41.571 94.247 99.201 1.00 43.48 S ATOM 8053 SG CYS A1406 41.983 90.729 97.844 1.00 47.50 S ATOM 8104 SG CYS A1414 38.207 92.683 97.500 1.00 40.99 S ATOM 8121 SG CYS A1417 40.861 93.151 95.074 1.00 36.65 S Time building chain proxies: 10.03, per 1000 atoms: 0.61 Number of scatterers: 16573 At special positions: 0 Unit cell: (107.73, 149.625, 134.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 58 16.00 P 34 15.00 O 3190 8.00 N 2871 7.00 C 10416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.49 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 121 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " Number of angles added : 21 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3646 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 21 sheets defined 40.0% alpha, 16.4% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 5.62 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.748A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 267 through 287 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.493A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 removed outlier: 5.776A pdb=" N GLY A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 350 through 353 removed outlier: 3.918A pdb=" N ILE A 353 " --> pdb=" O ASN A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 354 through 375 removed outlier: 3.520A pdb=" N PHE A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.532A pdb=" N LEU A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 569 through 580 removed outlier: 3.741A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 636 removed outlier: 3.630A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 631 through 636' Processing helix chain 'A' and resid 654 through 658 removed outlier: 3.641A pdb=" N CYS A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 658 " --> pdb=" O ARG A 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 658' Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 723 through 739 removed outlier: 3.669A pdb=" N HIS A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 758 Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 873 through 882 Processing helix chain 'A' and resid 909 through 914 removed outlier: 4.330A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 removed outlier: 3.801A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1399 removed outlier: 3.884A pdb=" N LEU A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1404 Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1463 through 1467 removed outlier: 3.628A pdb=" N PHE A1466 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.756A pdb=" N LYS A1493 " --> pdb=" O ILE A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1499 removed outlier: 3.613A pdb=" N ILE A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A1499 " --> pdb=" O LEU A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 Processing helix chain 'A' and resid 1583 through 1603 removed outlier: 3.519A pdb=" N ILE A1587 " --> pdb=" O PRO A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.614A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1673 through 1683 removed outlier: 3.513A pdb=" N ARG A1677 " --> pdb=" O PRO A1673 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 32 Processing helix chain 'B' and resid 37 through 59 removed outlier: 4.231A pdb=" N LYS B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.842A pdb=" N PHE B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.870A pdb=" N LYS B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 136 Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.583A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 190 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 208 through 224 removed outlier: 3.640A pdb=" N ALA B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 246 removed outlier: 4.354A pdb=" N ASP B 234 " --> pdb=" O HIS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.810A pdb=" N ILE B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 297 removed outlier: 3.547A pdb=" N LEU B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 322 Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 340 through 362 removed outlier: 4.081A pdb=" N TYR B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 451 removed outlier: 3.587A pdb=" N PHE B 437 " --> pdb=" O TYR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 469 Processing helix chain 'B' and resid 470 through 474 removed outlier: 3.807A pdb=" N PHE B 473 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 509 through 513 removed outlier: 3.611A pdb=" N GLU B 512 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 513 " --> pdb=" O PHE B 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 509 through 513' Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 547 through 552 Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.566A pdb=" N LEU B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 596 removed outlier: 3.808A pdb=" N SER B 596 " --> pdb=" O PRO B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.936A pdb=" N ALA B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.868A pdb=" N THR B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 691 removed outlier: 3.972A pdb=" N TRP B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.554A pdb=" N PHE B 703 " --> pdb=" O HIS B 699 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.857A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 18 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP A 195 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 13.759A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 4.113A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR A 9 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.302A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 7.154A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.601A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.601A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.866A pdb=" N VAL A 432 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AB2, first strand: chain 'A' and resid 533 through 534 removed outlier: 3.838A pdb=" N THR A 539 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.979A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.979A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB6, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.884A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.884A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS A 957 " --> pdb=" O ILE A1564 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE A1564 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU A 959 " --> pdb=" O ILE A1562 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE A1562 " --> pdb=" O GLU A 959 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 985 through 986 removed outlier: 6.679A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 425 through 431 Processing sheet with id=AC2, first strand: chain 'B' and resid 536 through 540 removed outlier: 5.193A pdb=" N THR B 660 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA B 626 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 585 through 587 removed outlier: 4.390A pdb=" N HIS B 585 " --> pdb=" O LYS B 599 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1854 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 6.78 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 2709 1.26 - 1.40: 4287 1.40 - 1.54: 9626 1.54 - 1.67: 308 1.67 - 1.81: 81 Bond restraints: 17011 Sorted by residual: bond pdb=" C PRO A1687 " pdb=" O PRO A1687 " ideal model delta sigma weight residual 1.233 1.125 0.108 1.19e-02 7.06e+03 8.21e+01 bond pdb=" C TRP A1688 " pdb=" O TRP A1688 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.33e-02 5.65e+03 1.73e+01 bond pdb=" C TYR A 921 " pdb=" N TYR A 922 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.07e-02 2.33e+03 1.10e+01 bond pdb=" N PRO A1690 " pdb=" CD PRO A1690 " ideal model delta sigma weight residual 1.474 1.430 0.044 1.40e-02 5.10e+03 9.94e+00 bond pdb=" N PHE A1691 " pdb=" CA PHE A1691 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.34e-02 5.57e+03 6.43e+00 ... (remaining 17006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 22070 1.96 - 3.92: 836 3.92 - 5.88: 138 5.88 - 7.84: 40 7.84 - 9.80: 13 Bond angle restraints: 23097 Sorted by residual: angle pdb=" C PRO A1687 " pdb=" CA PRO A1687 " pdb=" CB PRO A1687 " ideal model delta sigma weight residual 111.23 102.89 8.34 1.28e+00 6.10e-01 4.24e+01 angle pdb=" N PRO A1690 " pdb=" CD PRO A1690 " pdb=" CG PRO A1690 " ideal model delta sigma weight residual 103.80 97.07 6.73 1.20e+00 6.94e-01 3.15e+01 angle pdb=" N PRO A1687 " pdb=" CA PRO A1687 " pdb=" C PRO A1687 " ideal model delta sigma weight residual 111.21 118.89 -7.68 1.59e+00 3.96e-01 2.33e+01 angle pdb=" C SER A 396 " pdb=" N GLU A 397 " pdb=" CA GLU A 397 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" CA ASN A1649 " pdb=" CB ASN A1649 " pdb=" CG ASN A1649 " ideal model delta sigma weight residual 112.60 117.07 -4.47 1.00e+00 1.00e+00 2.00e+01 ... (remaining 23092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.95: 9890 34.95 - 69.91: 356 69.91 - 104.86: 27 104.86 - 139.82: 1 139.82 - 174.77: 9 Dihedral angle restraints: 10283 sinusoidal: 4611 harmonic: 5672 Sorted by residual: dihedral pdb=" CA GLU A1650 " pdb=" C GLU A1650 " pdb=" N GLU A1651 " pdb=" CA GLU A1651 " ideal model delta harmonic sigma weight residual 180.00 -124.45 -55.55 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 34.55 165.45 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' U D 8 " pdb=" C1' U D 8 " pdb=" N1 U D 8 " pdb=" C2 U D 8 " ideal model delta sinusoidal sigma weight residual 200.00 39.73 160.27 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 10280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1859 0.059 - 0.118: 500 0.118 - 0.177: 111 0.177 - 0.236: 15 0.236 - 0.294: 8 Chirality restraints: 2493 Sorted by residual: chirality pdb=" CA ASN A1649 " pdb=" N ASN A1649 " pdb=" C ASN A1649 " pdb=" CB ASN A1649 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB VAL A 377 " pdb=" CA VAL A 377 " pdb=" CG1 VAL A 377 " pdb=" CG2 VAL A 377 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1' C D 13 " pdb=" O4' C D 13 " pdb=" C2' C D 13 " pdb=" N1 C D 13 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2490 not shown) Planarity restraints: 2854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 962 " -0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO A 963 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 963 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 963 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 297 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ALA A 297 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA A 297 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 298 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 700 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.95e+00 pdb=" N PRO B 701 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 701 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 701 " 0.045 5.00e-02 4.00e+02 ... (remaining 2851 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 574 2.71 - 3.25: 14512 3.25 - 3.80: 24888 3.80 - 4.35: 31649 4.35 - 4.90: 54924 Nonbonded interactions: 126547 Sorted by model distance: nonbonded pdb=" O SER A 449 " pdb=" OG SER A 449 " model vdw 2.157 3.040 nonbonded pdb=" O THR B 87 " pdb=" OG1 THR B 87 " model vdw 2.266 3.040 nonbonded pdb=" O ASN A 179 " pdb=" O2' G D -3 " model vdw 2.268 3.040 nonbonded pdb=" O THR A 969 " pdb=" OG1 THR A 969 " model vdw 2.269 3.040 nonbonded pdb=" O PHE A 104 " pdb=" O2' G D -9 " model vdw 2.318 3.040 ... (remaining 126542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.320 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 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 : 0.009 0.108 17011 Z= 0.562 Angle : 0.931 9.797 23097 Z= 0.520 Chirality : 0.059 0.294 2493 Planarity : 0.008 0.089 2854 Dihedral : 17.819 174.774 6637 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 2.74 % Allowed : 11.42 % Favored : 85.85 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.27 % Twisted General : 0.11 % 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: -2.88 (0.15), residues: 1953 helix: -1.78 (0.15), residues: 686 sheet: -0.49 (0.31), residues: 248 loop : -2.41 (0.15), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 612 HIS 0.018 0.002 HIS A 915 PHE 0.034 0.003 PHE B 324 TYR 0.029 0.003 TYR B 607 ARG 0.007 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 414 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7618 (t0) cc_final: 0.7400 (t0) REVERT: A 708 ASN cc_start: 0.6887 (t0) cc_final: 0.6611 (t0) REVERT: A 784 GLU cc_start: 0.6149 (mt-10) cc_final: 0.5929 (mt-10) REVERT: A 938 ASP cc_start: 0.7147 (p0) cc_final: 0.6857 (p0) REVERT: A 1504 GLU cc_start: 0.5850 (tp30) cc_final: 0.5628 (tp30) REVERT: A 1570 PHE cc_start: 0.7967 (p90) cc_final: 0.7601 (p90) REVERT: B 16 ARG cc_start: 0.7210 (ptp90) cc_final: 0.6869 (ptp90) REVERT: B 22 LYS cc_start: 0.7449 (ttmm) cc_final: 0.7219 (ttmm) REVERT: B 141 ASP cc_start: 0.7017 (p0) cc_final: 0.6730 (p0) REVERT: B 144 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7725 (mtpt) REVERT: B 409 LYS cc_start: 0.8193 (mttt) cc_final: 0.7985 (mtmt) REVERT: B 589 ASN cc_start: 0.8042 (t0) cc_final: 0.7778 (t0) REVERT: B 638 VAL cc_start: 0.7755 (p) cc_final: 0.7505 (t) REVERT: B 640 ASP cc_start: 0.7523 (p0) cc_final: 0.7308 (p0) outliers start: 47 outliers final: 12 residues processed: 449 average time/residue: 1.4290 time to fit residues: 709.0990 Evaluate side-chains 345 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 333 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 568 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 160 HIS A 287 ASN A 306 HIS A 664 ASN A 871 ASN A 881 ASN A 993 ASN A1506 ASN A1516 ASN A1604 ASN B 109 ASN B 112 ASN B 142 ASN B 194 ASN B 210 HIS B 446 ASN B 513 ASN B 514 HIS B 572 ASN B 576 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17011 Z= 0.246 Angle : 0.656 9.357 23097 Z= 0.343 Chirality : 0.045 0.290 2493 Planarity : 0.006 0.057 2854 Dihedral : 15.608 177.392 2677 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 3.79 % Allowed : 19.98 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 1953 helix: 0.38 (0.19), residues: 690 sheet: -0.46 (0.29), residues: 273 loop : -1.95 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 82 HIS 0.011 0.002 HIS A 915 PHE 0.015 0.002 PHE A 824 TYR 0.018 0.002 TYR B 607 ARG 0.009 0.001 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 397 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 PHE cc_start: 0.8046 (m-10) cc_final: 0.7843 (m-80) REVERT: A 198 ASP cc_start: 0.7378 (p0) cc_final: 0.7074 (p0) REVERT: A 313 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7582 (mtmm) REVERT: A 581 GLU cc_start: 0.6483 (pp20) cc_final: 0.6257 (pp20) REVERT: A 806 ASP cc_start: 0.7701 (p0) cc_final: 0.7488 (p0) REVERT: A 847 ASP cc_start: 0.7057 (m-30) cc_final: 0.6836 (m-30) REVERT: A 1436 TYR cc_start: 0.7465 (t80) cc_final: 0.7134 (t80) REVERT: A 1570 PHE cc_start: 0.8292 (p90) cc_final: 0.7954 (p90) REVERT: A 1596 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7747 (mm110) REVERT: B 102 GLU cc_start: 0.6793 (tp30) cc_final: 0.6366 (tp30) REVERT: B 124 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7359 (tp) REVERT: B 139 LYS cc_start: 0.7892 (mptt) cc_final: 0.7596 (mptt) REVERT: B 144 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7682 (mtpt) REVERT: B 318 ASP cc_start: 0.7545 (t70) cc_final: 0.7330 (t70) REVERT: B 467 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6765 (tp30) REVERT: B 472 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7196 (pp) REVERT: B 640 ASP cc_start: 0.7608 (p0) cc_final: 0.7381 (p0) REVERT: B 663 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7930 (ttpp) REVERT: B 691 THR cc_start: 0.8592 (p) cc_final: 0.8367 (m) outliers start: 65 outliers final: 24 residues processed: 424 average time/residue: 1.4961 time to fit residues: 698.1479 Evaluate side-chains 376 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 349 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1676 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 180 optimal weight: 0.0070 chunk 194 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 178 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 138 ASN A 534 ASN A 984 HIS A1506 ASN A1649 ASN B 194 ASN B 210 HIS B 457 HIS B 513 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17011 Z= 0.164 Angle : 0.560 8.186 23097 Z= 0.291 Chirality : 0.042 0.244 2493 Planarity : 0.005 0.053 2854 Dihedral : 15.327 176.441 2666 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 3.79 % Allowed : 22.89 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 1953 helix: 1.25 (0.20), residues: 698 sheet: -0.13 (0.30), residues: 273 loop : -1.62 (0.17), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 82 HIS 0.007 0.001 HIS A 915 PHE 0.016 0.001 PHE B 491 TYR 0.019 0.001 TYR A1436 ARG 0.006 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 349 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7491 (p0) cc_final: 0.7238 (p0) REVERT: A 236 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7766 (ttm170) REVERT: A 372 LYS cc_start: 0.8169 (tppp) cc_final: 0.7895 (ttmm) REVERT: A 511 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7965 (mtt180) REVERT: A 628 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7444 (mtm-85) REVERT: A 969 THR cc_start: 0.8021 (t) cc_final: 0.7793 (m) REVERT: A 1436 TYR cc_start: 0.7793 (t80) cc_final: 0.7556 (t80) REVERT: A 1596 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7804 (mm110) REVERT: B 124 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7374 (tp) REVERT: B 141 ASP cc_start: 0.6628 (p0) cc_final: 0.6288 (p0) REVERT: B 144 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7551 (mtmt) REVERT: B 263 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7140 (ttm-80) REVERT: B 472 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7172 (pp) REVERT: B 595 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7501 (mtm180) REVERT: B 663 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7915 (ttpp) REVERT: B 691 THR cc_start: 0.8600 (p) cc_final: 0.8386 (m) outliers start: 65 outliers final: 23 residues processed: 381 average time/residue: 1.4223 time to fit residues: 598.1995 Evaluate side-chains 366 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 338 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 306 HIS A 984 HIS A1506 ASN A1544 ASN B 210 HIS B 448 ASN B 513 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17011 Z= 0.317 Angle : 0.663 8.719 23097 Z= 0.344 Chirality : 0.046 0.288 2493 Planarity : 0.005 0.056 2854 Dihedral : 15.505 174.424 2665 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.17 % Favored : 94.78 % Rotamer: Outliers : 4.14 % Allowed : 23.06 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 1953 helix: 1.51 (0.20), residues: 685 sheet: -0.03 (0.30), residues: 263 loop : -1.60 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 556 HIS 0.009 0.002 HIS A 109 PHE 0.020 0.002 PHE B 324 TYR 0.025 0.002 TYR A 149 ARG 0.006 0.001 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 390 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6744 (mp0) cc_final: 0.6541 (mp0) REVERT: A 52 THR cc_start: 0.8169 (p) cc_final: 0.7932 (t) REVERT: A 168 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7685 (mtm180) REVERT: A 174 SER cc_start: 0.8413 (t) cc_final: 0.8166 (p) REVERT: A 236 ARG cc_start: 0.7917 (ttm170) cc_final: 0.7714 (ttm170) REVERT: A 348 GLN cc_start: 0.8219 (tp40) cc_final: 0.8015 (mm-40) REVERT: A 511 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8179 (mtt180) REVERT: A 627 MET cc_start: 0.8017 (mmm) cc_final: 0.7315 (mmm) REVERT: A 628 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8231 (mtm110) REVERT: A 918 LYS cc_start: 0.8162 (mptt) cc_final: 0.7939 (mmtp) REVERT: A 1489 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7399 (mt) REVERT: A 1504 GLU cc_start: 0.6337 (tp30) cc_final: 0.6122 (tp30) REVERT: A 1593 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7760 (mttm) REVERT: A 1596 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7120 (mt0) REVERT: B 55 LEU cc_start: 0.8319 (tp) cc_final: 0.8109 (mp) REVERT: B 124 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7586 (tp) REVERT: B 137 ARG cc_start: 0.6600 (tpp-160) cc_final: 0.6279 (tpp-160) REVERT: B 144 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7566 (mtmt) REVERT: B 222 SER cc_start: 0.8381 (t) cc_final: 0.8078 (p) REVERT: B 472 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7436 (pp) REVERT: B 566 SER cc_start: 0.7756 (t) cc_final: 0.7348 (p) REVERT: B 595 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7555 (mtm180) REVERT: B 618 LYS cc_start: 0.8236 (mptt) cc_final: 0.7983 (mmmm) REVERT: B 663 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7996 (ttpp) REVERT: B 691 THR cc_start: 0.8619 (p) cc_final: 0.8401 (m) outliers start: 71 outliers final: 29 residues processed: 424 average time/residue: 1.4893 time to fit residues: 697.3387 Evaluate side-chains 402 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 367 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 1460 GLU Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 132 optimal weight: 0.0030 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 171 optimal weight: 0.0170 chunk 48 optimal weight: 2.9990 overall best weight: 0.5430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS A 348 GLN A 350 ASN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 778 ASN A1506 ASN A1592 ASN B 210 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17011 Z= 0.166 Angle : 0.556 9.284 23097 Z= 0.290 Chirality : 0.042 0.257 2493 Planarity : 0.004 0.054 2854 Dihedral : 15.297 174.921 2665 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 2.80 % Allowed : 25.63 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 1953 helix: 1.83 (0.20), residues: 690 sheet: 0.10 (0.30), residues: 270 loop : -1.42 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 612 HIS 0.009 0.001 HIS A 328 PHE 0.017 0.001 PHE B 491 TYR 0.013 0.001 TYR A 149 ARG 0.006 0.000 ARG A 738 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 371 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8128 (mtt180) REVERT: A 627 MET cc_start: 0.7951 (mmm) cc_final: 0.7171 (mmm) REVERT: A 628 ARG cc_start: 0.8570 (mtm-85) cc_final: 0.8214 (mtm110) REVERT: A 1489 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7386 (mt) REVERT: A 1504 GLU cc_start: 0.6347 (tp30) cc_final: 0.6133 (tp30) REVERT: A 1570 PHE cc_start: 0.8431 (p90) cc_final: 0.8023 (p90) REVERT: A 1593 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7651 (mttm) REVERT: B 55 LEU cc_start: 0.8254 (tp) cc_final: 0.7987 (mp) REVERT: B 124 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7546 (tp) REVERT: B 137 ARG cc_start: 0.6601 (tpp-160) cc_final: 0.6324 (tpp-160) REVERT: B 144 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7541 (mtmt) REVERT: B 472 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7304 (pp) REVERT: B 497 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7640 (mt) REVERT: B 508 LYS cc_start: 0.8266 (mmmm) cc_final: 0.7881 (mmmm) REVERT: B 618 LYS cc_start: 0.8218 (mptt) cc_final: 0.7974 (mmmm) REVERT: B 663 LYS cc_start: 0.8237 (ttmm) cc_final: 0.7984 (ttpp) outliers start: 48 outliers final: 19 residues processed: 396 average time/residue: 1.4681 time to fit residues: 640.3885 Evaluate side-chains 378 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 354 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 328 HIS A 778 ASN A1506 ASN A1568 HIS A1592 ASN B 210 HIS B 513 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17011 Z= 0.259 Angle : 0.615 11.424 23097 Z= 0.319 Chirality : 0.044 0.254 2493 Planarity : 0.005 0.062 2854 Dihedral : 15.346 173.453 2665 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 3.26 % Allowed : 25.98 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 1953 helix: 1.83 (0.20), residues: 692 sheet: 0.27 (0.31), residues: 259 loop : -1.40 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 612 HIS 0.009 0.001 HIS A 328 PHE 0.015 0.002 PHE B 324 TYR 0.023 0.002 TYR A 149 ARG 0.007 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 369 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8416 (mtpt) REVERT: A 174 SER cc_start: 0.8434 (t) cc_final: 0.8158 (p) REVERT: A 511 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8137 (mtt180) REVERT: A 627 MET cc_start: 0.8014 (mmm) cc_final: 0.7348 (mmm) REVERT: A 628 ARG cc_start: 0.8619 (mtm-85) cc_final: 0.8349 (mtm110) REVERT: A 1472 GLU cc_start: 0.6399 (mp0) cc_final: 0.6188 (mp0) REVERT: A 1489 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7401 (mt) REVERT: A 1504 GLU cc_start: 0.6379 (tp30) cc_final: 0.6163 (tp30) REVERT: A 1592 ASN cc_start: 0.7920 (m-40) cc_final: 0.7720 (m110) REVERT: A 1593 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7710 (mttm) REVERT: A 1596 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: A 1617 HIS cc_start: 0.7956 (p-80) cc_final: 0.7450 (p-80) REVERT: B 55 LEU cc_start: 0.8270 (tp) cc_final: 0.8015 (mp) REVERT: B 124 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7608 (tp) REVERT: B 137 ARG cc_start: 0.6630 (tpp-160) cc_final: 0.6392 (tpp-160) REVERT: B 144 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7540 (mtmt) REVERT: B 222 SER cc_start: 0.8385 (t) cc_final: 0.8104 (p) REVERT: B 472 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7367 (pp) REVERT: B 497 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7672 (mt) REVERT: B 508 LYS cc_start: 0.8260 (mmmm) cc_final: 0.7796 (mmmm) REVERT: B 512 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6872 (mt-10) REVERT: B 562 LYS cc_start: 0.6909 (ptpt) cc_final: 0.6655 (ptpt) REVERT: B 566 SER cc_start: 0.7868 (OUTLIER) cc_final: 0.7361 (p) REVERT: B 618 LYS cc_start: 0.8234 (mptt) cc_final: 0.7976 (mmmm) REVERT: B 636 SER cc_start: 0.8178 (p) cc_final: 0.7813 (t) REVERT: B 663 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7993 (ttpp) outliers start: 56 outliers final: 28 residues processed: 394 average time/residue: 1.4963 time to fit residues: 648.9735 Evaluate side-chains 396 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 360 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1460 GLU Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 190 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 328 HIS A 350 ASN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 GLN A 778 ASN A 905 HIS A1506 ASN B 210 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17011 Z= 0.189 Angle : 0.566 9.009 23097 Z= 0.296 Chirality : 0.042 0.242 2493 Planarity : 0.005 0.064 2854 Dihedral : 15.256 173.834 2665 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 3.32 % Allowed : 26.79 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 1953 helix: 2.03 (0.20), residues: 689 sheet: 0.34 (0.31), residues: 258 loop : -1.33 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 612 HIS 0.009 0.001 HIS A 328 PHE 0.017 0.001 PHE B 491 TYR 0.016 0.001 TYR A 149 ARG 0.007 0.000 ARG A 738 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 357 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8410 (mtpt) REVERT: A 174 SER cc_start: 0.8430 (t) cc_final: 0.8142 (p) REVERT: A 415 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: A 511 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8126 (mtt180) REVERT: A 627 MET cc_start: 0.7980 (mmm) cc_final: 0.7277 (mmm) REVERT: A 639 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6619 (tm-30) REVERT: A 668 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: A 1504 GLU cc_start: 0.6363 (tp30) cc_final: 0.6148 (tp30) REVERT: A 1570 PHE cc_start: 0.8479 (p90) cc_final: 0.8001 (p90) REVERT: A 1593 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7759 (mttm) REVERT: A 1596 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7875 (mm110) REVERT: B 124 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7607 (tp) REVERT: B 144 LYS cc_start: 0.7940 (ttmt) cc_final: 0.7527 (mtmt) REVERT: B 472 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7361 (pp) REVERT: B 497 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7642 (mt) REVERT: B 508 LYS cc_start: 0.8233 (mmmm) cc_final: 0.7773 (mmmm) REVERT: B 512 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6734 (mt-10) REVERT: B 566 SER cc_start: 0.7769 (m) cc_final: 0.7287 (p) REVERT: B 636 SER cc_start: 0.8145 (p) cc_final: 0.7778 (t) REVERT: B 663 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7985 (ttpp) outliers start: 57 outliers final: 28 residues processed: 388 average time/residue: 1.4960 time to fit residues: 639.8175 Evaluate side-chains 393 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 357 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 668 GLN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain A residue 1692 GLN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 2.9990 chunk 76 optimal weight: 0.0470 chunk 113 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 328 HIS A 668 GLN A 778 ASN A1506 ASN A1592 ASN B 210 HIS B 513 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17011 Z= 0.175 Angle : 0.563 8.338 23097 Z= 0.294 Chirality : 0.042 0.235 2493 Planarity : 0.005 0.064 2854 Dihedral : 15.218 173.599 2665 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 2.80 % Allowed : 27.49 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 1953 helix: 2.13 (0.20), residues: 689 sheet: 0.38 (0.31), residues: 262 loop : -1.28 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.008 0.001 HIS A 328 PHE 0.017 0.001 PHE B 491 TYR 0.015 0.001 TYR A 149 ARG 0.007 0.000 ARG A1644 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 362 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: A 55 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (mtpt) REVERT: A 174 SER cc_start: 0.8421 (t) cc_final: 0.8145 (p) REVERT: A 415 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: A 511 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8125 (mtt180) REVERT: A 627 MET cc_start: 0.7997 (mmm) cc_final: 0.7263 (mmm) REVERT: A 639 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6612 (tm-30) REVERT: A 668 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A 1456 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8374 (mp) REVERT: A 1472 GLU cc_start: 0.6271 (mp0) cc_final: 0.5986 (mp0) REVERT: A 1504 GLU cc_start: 0.6345 (tp30) cc_final: 0.6134 (tp30) REVERT: A 1570 PHE cc_start: 0.8476 (p90) cc_final: 0.7969 (p90) REVERT: A 1593 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7769 (mttm) REVERT: A 1596 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7865 (mm110) REVERT: B 102 GLU cc_start: 0.6730 (tp30) cc_final: 0.6297 (tp30) REVERT: B 124 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7627 (tp) REVERT: B 144 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7512 (mtmt) REVERT: B 263 ARG cc_start: 0.7402 (ttp80) cc_final: 0.7131 (ttm-80) REVERT: B 472 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7277 (pp) REVERT: B 497 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7619 (mt) REVERT: B 508 LYS cc_start: 0.8212 (mmmm) cc_final: 0.7756 (mmmm) REVERT: B 512 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6760 (mt-10) REVERT: B 566 SER cc_start: 0.7711 (OUTLIER) cc_final: 0.7215 (p) REVERT: B 595 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7546 (mtm180) REVERT: B 636 SER cc_start: 0.7981 (p) cc_final: 0.7656 (t) REVERT: B 663 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7965 (ttpp) REVERT: B 690 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6525 (mp0) outliers start: 48 outliers final: 27 residues processed: 387 average time/residue: 1.4845 time to fit residues: 632.7731 Evaluate side-chains 396 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 356 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 668 GLN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 328 HIS A 350 ASN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 GLN A 778 ASN A1506 ASN B 210 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17011 Z= 0.208 Angle : 0.576 8.356 23097 Z= 0.301 Chirality : 0.042 0.234 2493 Planarity : 0.005 0.065 2854 Dihedral : 15.227 173.377 2665 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 3.09 % Allowed : 27.26 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1953 helix: 2.16 (0.20), residues: 689 sheet: 0.42 (0.32), residues: 262 loop : -1.27 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.008 0.001 HIS A 328 PHE 0.015 0.001 PHE B 491 TYR 0.018 0.001 TYR A 149 ARG 0.008 0.000 ARG A1644 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 362 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: A 55 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8425 (mtpt) REVERT: A 174 SER cc_start: 0.8420 (t) cc_final: 0.8161 (p) REVERT: A 494 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7932 (m) REVERT: A 511 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8127 (mtt180) REVERT: A 627 MET cc_start: 0.8028 (mmm) cc_final: 0.7399 (mmm) REVERT: A 639 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6599 (tm-30) REVERT: A 668 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: A 1504 GLU cc_start: 0.6352 (tp30) cc_final: 0.6143 (tp30) REVERT: A 1570 PHE cc_start: 0.8502 (p90) cc_final: 0.8005 (p90) REVERT: A 1596 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7862 (mm110) REVERT: B 102 GLU cc_start: 0.6723 (tp30) cc_final: 0.6297 (tp30) REVERT: B 124 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7638 (tp) REVERT: B 144 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7517 (mtmt) REVERT: B 263 ARG cc_start: 0.7399 (ttp80) cc_final: 0.7126 (ttm-80) REVERT: B 472 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7354 (pp) REVERT: B 497 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7647 (mt) REVERT: B 508 LYS cc_start: 0.8219 (mmmm) cc_final: 0.7739 (mmmm) REVERT: B 512 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6711 (mt-10) REVERT: B 566 SER cc_start: 0.7709 (OUTLIER) cc_final: 0.7215 (p) REVERT: B 595 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7559 (mtm180) REVERT: B 636 SER cc_start: 0.8006 (p) cc_final: 0.7676 (t) REVERT: B 663 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7932 (ttpp) REVERT: B 690 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6539 (mp0) outliers start: 53 outliers final: 32 residues processed: 390 average time/residue: 1.4672 time to fit residues: 630.0668 Evaluate side-chains 400 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 356 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 668 GLN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 121 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 124 optimal weight: 0.1980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 306 HIS A 328 HIS ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 GLN A 778 ASN A1506 ASN B 210 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17011 Z= 0.252 Angle : 0.600 8.581 23097 Z= 0.312 Chirality : 0.043 0.234 2493 Planarity : 0.005 0.066 2854 Dihedral : 15.275 174.632 2665 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 3.15 % Allowed : 27.49 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1953 helix: 2.11 (0.20), residues: 690 sheet: 0.42 (0.32), residues: 258 loop : -1.29 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.009 0.001 HIS A 328 PHE 0.014 0.002 PHE B 324 TYR 0.021 0.001 TYR A 149 ARG 0.009 0.000 ARG A1644 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 369 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: A 55 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8456 (mtpt) REVERT: A 78 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7869 (p0) REVERT: A 174 SER cc_start: 0.8427 (t) cc_final: 0.8170 (p) REVERT: A 415 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: A 494 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7942 (m) REVERT: A 511 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8133 (mtt180) REVERT: A 627 MET cc_start: 0.8110 (mmm) cc_final: 0.7434 (mmm) REVERT: A 639 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6606 (tm-30) REVERT: A 668 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: A 1504 GLU cc_start: 0.6368 (tp30) cc_final: 0.6159 (tp30) REVERT: A 1596 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7873 (mm110) REVERT: A 1623 ASP cc_start: 0.7152 (t0) cc_final: 0.6909 (t0) REVERT: B 102 GLU cc_start: 0.6713 (tp30) cc_final: 0.6295 (tp30) REVERT: B 124 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7648 (tp) REVERT: B 137 ARG cc_start: 0.6662 (tpp-160) cc_final: 0.6429 (tpp-160) REVERT: B 144 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7513 (mtmt) REVERT: B 222 SER cc_start: 0.8374 (t) cc_final: 0.8076 (p) REVERT: B 472 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7382 (pp) REVERT: B 497 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7681 (mt) REVERT: B 508 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7752 (mmmm) REVERT: B 566 SER cc_start: 0.7755 (OUTLIER) cc_final: 0.7253 (p) REVERT: B 595 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7571 (mtm180) REVERT: B 636 SER cc_start: 0.8067 (p) cc_final: 0.7706 (t) REVERT: B 663 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7904 (ttpp) REVERT: B 690 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6534 (mp0) outliers start: 54 outliers final: 31 residues processed: 397 average time/residue: 1.4780 time to fit residues: 646.9062 Evaluate side-chains 411 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 366 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 668 GLN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 157 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 138 optimal weight: 3.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 306 HIS A 328 HIS A 350 ASN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 ASN A1506 ASN A1592 ASN B 210 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102549 restraints weight = 22502.489| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.94 r_work: 0.3143 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 17011 Z= 0.258 Angle : 0.822 59.200 23097 Z= 0.484 Chirality : 0.046 0.673 2493 Planarity : 0.005 0.100 2854 Dihedral : 15.279 174.356 2665 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 2.91 % Allowed : 27.78 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1953 helix: 2.11 (0.20), residues: 690 sheet: 0.42 (0.32), residues: 258 loop : -1.29 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.008 0.001 HIS A 328 PHE 0.014 0.001 PHE B 324 TYR 0.020 0.001 TYR A 149 ARG 0.008 0.000 ARG A1644 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9139.47 seconds wall clock time: 162 minutes 44.99 seconds (9764.99 seconds total)