Starting phenix.real_space_refine on Sun Jun 15 01:22:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xsq_33431/06_2025/7xsq_33431.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xsq_33431/06_2025/7xsq_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/cci-nas-00/data/ceres_data/7xsq_33431/06_2025/7xsq_33431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xsq_33431/06_2025/7xsq_33431.map" model { file = "/net/cci-nas-00/data/ceres_data/7xsq_33431/06_2025/7xsq_33431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xsq_33431/06_2025/7xsq_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.37, per 1000 atoms: 0.63 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: 4.38 Conformation dependent library (CDL) restraints added in 2.0 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: 6.00 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: 6.86 Time building geometry restraints manager: 5.19 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: 3.810 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: 2.960 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 48.850 Find NCS groups from input model: 0.170 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.480 ------------------------------------------------------------------------------- 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 : 0.010 0.228 17027 Z= 0.400 Angle : 1.002 22.746 23118 Z= 0.524 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 Details of bonding type rmsd hydrogen bonds : bond 0.17052 ( 625) hydrogen bonds : angle 5.80984 ( 1854) metal coordination : bond 0.13659 ( 16) metal coordination : angle 12.36578 ( 21) covalent geometry : bond 0.00865 (17011) covalent geometry : angle 0.93064 (23097) *********************** 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 : 1.892 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: 1.4131 time to fit residues: 705.0298 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 : 1.811 ------------------------------------------------------------------------------- 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: 5.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110294 restraints weight = 22806.063| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.03 r_work: 0.3265 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 17027 Z= 0.178 Angle : 0.669 12.990 23118 Z= 0.344 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 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 625) hydrogen bonds : angle 4.42337 ( 1854) metal coordination : bond 0.01840 ( 16) metal coordination : angle 4.43789 ( 21) covalent geometry : bond 0.00378 (17011) covalent geometry : angle 0.65580 (23097) *********************** 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 : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 PHE cc_start: 0.8164 (m-10) cc_final: 0.7802 (m-80) REVERT: A 196 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7671 (mt-10) REVERT: A 198 ASP cc_start: 0.7787 (p0) cc_final: 0.7477 (p0) REVERT: A 230 LEU cc_start: 0.7764 (tp) cc_final: 0.7527 (tt) REVERT: A 313 LYS cc_start: 0.8074 (mtmm) cc_final: 0.7779 (mtmm) REVERT: A 523 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 567 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8415 (ptpp) REVERT: A 581 GLU cc_start: 0.7135 (pp20) cc_final: 0.6889 (pp20) REVERT: A 693 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 696 ASN cc_start: 0.6337 (p0) cc_final: 0.6129 (p0) REVERT: A 784 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6851 (mt-10) REVERT: A 806 ASP cc_start: 0.8400 (p0) cc_final: 0.8199 (p0) REVERT: A 847 ASP cc_start: 0.7667 (m-30) cc_final: 0.7426 (m-30) REVERT: A 938 ASP cc_start: 0.7839 (p0) cc_final: 0.7588 (p0) REVERT: A 1436 TYR cc_start: 0.7782 (t80) cc_final: 0.7387 (t80) REVERT: A 1460 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7548 (mt-10) REVERT: A 1570 PHE cc_start: 0.8338 (p90) cc_final: 0.7948 (p90) REVERT: A 1596 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8030 (mm110) REVERT: B 58 GLU cc_start: 0.7877 (tt0) cc_final: 0.7675 (tt0) REVERT: B 102 GLU cc_start: 0.7664 (tp30) cc_final: 0.7187 (tp30) REVERT: B 124 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7588 (tp) REVERT: B 139 LYS cc_start: 0.8097 (mptt) cc_final: 0.7708 (mptt) REVERT: B 144 LYS cc_start: 0.8413 (ttmt) cc_final: 0.7806 (mtpt) REVERT: B 318 ASP cc_start: 0.8214 (t70) cc_final: 0.7958 (t70) REVERT: B 467 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7420 (tp30) REVERT: B 472 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7340 (pp) REVERT: B 640 ASP cc_start: 0.7645 (p0) cc_final: 0.7422 (p0) REVERT: B 663 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8261 (ttpp) REVERT: B 686 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7642 (mt-10) REVERT: B 691 THR cc_start: 0.8763 (p) cc_final: 0.8544 (m) outliers start: 65 outliers final: 24 residues processed: 424 average time/residue: 1.6292 time to fit residues: 762.9266 Evaluate side-chains 377 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 350 time to evaluate : 1.807 ------------------------------------------------------------------------------- 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 189 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 76 optimal weight: 0.0270 chunk 182 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 187 optimal weight: 0.0870 chunk 78 optimal weight: 2.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- 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 306 HIS A 534 ASN A 789 HIS A 984 HIS A 993 ASN A1506 ASN A1544 ASN A1649 ASN B 210 HIS B 448 ASN B 457 HIS B 513 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101823 restraints weight = 22378.777| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.95 r_work: 0.3130 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17027 Z= 0.224 Angle : 0.699 9.302 23118 Z= 0.355 Chirality : 0.047 0.289 2493 Planarity : 0.006 0.056 2854 Dihedral : 15.607 176.789 2666 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 4.08 % Allowed : 22.71 % Favored : 73.21 % 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: -0.74 (0.18), residues: 1953 helix: 1.06 (0.20), residues: 694 sheet: -0.22 (0.30), residues: 266 loop : -1.76 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 82 HIS 0.009 0.002 HIS A 727 PHE 0.019 0.002 PHE B 324 TYR 0.024 0.002 TYR A 149 ARG 0.010 0.001 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.06103 ( 625) hydrogen bonds : angle 4.43239 ( 1854) metal coordination : bond 0.00752 ( 16) metal coordination : angle 4.73358 ( 21) covalent geometry : bond 0.00541 (17011) covalent geometry : angle 0.68438 (23097) *********************** 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 453 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 383 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.6381 (tpt) cc_final: 0.6110 (mmm) REVERT: A 168 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7850 (mtm180) REVERT: A 230 LEU cc_start: 0.8224 (tp) cc_final: 0.7930 (tt) REVERT: A 236 ARG cc_start: 0.8439 (ttm170) cc_final: 0.8187 (ttm170) REVERT: A 288 ASP cc_start: 0.7561 (t0) cc_final: 0.7352 (t0) REVERT: A 511 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8422 (mtt180) REVERT: A 528 ARG cc_start: 0.8512 (mtt180) cc_final: 0.8296 (mmm160) REVERT: A 628 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8204 (mtm110) REVERT: A 656 GLU cc_start: 0.7840 (pm20) cc_final: 0.7592 (pm20) REVERT: A 696 ASN cc_start: 0.6588 (p0) cc_final: 0.6306 (p0) REVERT: A 714 ILE cc_start: 0.8157 (pt) cc_final: 0.7908 (mm) REVERT: A 784 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7301 (mt-10) REVERT: A 1504 GLU cc_start: 0.6956 (tp30) cc_final: 0.6735 (tp30) REVERT: A 1566 SER cc_start: 0.8285 (m) cc_final: 0.8085 (p) REVERT: A 1586 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.6524 (m-30) REVERT: A 1593 LYS cc_start: 0.8325 (ttmm) cc_final: 0.8082 (mttt) REVERT: A 1596 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7480 (mt0) REVERT: B 124 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7767 (tp) REVERT: B 137 ARG cc_start: 0.7001 (tpp-160) cc_final: 0.6616 (tpp-160) REVERT: B 141 ASP cc_start: 0.7155 (p0) cc_final: 0.6770 (p0) REVERT: B 144 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7693 (mtmt) REVERT: B 222 SER cc_start: 0.8496 (t) cc_final: 0.8197 (p) REVERT: B 318 ASP cc_start: 0.8216 (t70) cc_final: 0.8005 (t70) REVERT: B 472 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7536 (pp) REVERT: B 568 ASP cc_start: 0.7320 (p0) cc_final: 0.7057 (p0) REVERT: B 595 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7998 (mtm180) REVERT: B 628 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: B 663 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8420 (ttpp) REVERT: B 686 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7330 (mt-10) outliers start: 70 outliers final: 29 residues processed: 415 average time/residue: 1.4086 time to fit residues: 644.8322 Evaluate side-chains 391 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 355 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 518 VAL 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 1489 ILE Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1586 ASP 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 162 THR Chi-restraints excluded: chain B residue 188 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 123 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 0.1980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 306 HIS A 328 HIS A 433 GLN A 459 ASN A 984 HIS A1506 ASN A1592 ASN B 210 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104528 restraints weight = 22512.785| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.96 r_work: 0.3180 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17027 Z= 0.113 Angle : 0.576 9.070 23118 Z= 0.296 Chirality : 0.042 0.258 2493 Planarity : 0.005 0.051 2854 Dihedral : 15.365 175.720 2665 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.03 % Rotamer: Outliers : 3.32 % Allowed : 24.29 % Favored : 72.39 % 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: -0.25 (0.18), residues: 1953 helix: 1.56 (0.20), residues: 694 sheet: -0.03 (0.30), residues: 275 loop : -1.54 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 82 HIS 0.009 0.001 HIS A 328 PHE 0.017 0.001 PHE B 491 TYR 0.015 0.001 TYR A 149 ARG 0.006 0.000 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 625) hydrogen bonds : angle 4.10509 ( 1854) metal coordination : bond 0.00345 ( 16) metal coordination : angle 3.56961 ( 21) covalent geometry : bond 0.00246 (17011) covalent geometry : angle 0.56593 (23097) *********************** 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 423 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 366 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 THR cc_start: 0.8315 (p) cc_final: 0.8098 (t) REVERT: A 168 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7846 (mtm180) REVERT: A 230 LEU cc_start: 0.8252 (tp) cc_final: 0.7984 (tt) REVERT: A 236 ARG cc_start: 0.8369 (ttm170) cc_final: 0.8148 (ttm170) REVERT: A 288 ASP cc_start: 0.7420 (t0) cc_final: 0.7202 (t0) REVERT: A 387 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8154 (p) REVERT: A 415 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: A 511 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8367 (mtt180) REVERT: A 628 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8170 (mtm110) REVERT: A 656 GLU cc_start: 0.7719 (pm20) cc_final: 0.7479 (pm20) REVERT: A 696 ASN cc_start: 0.6665 (p0) cc_final: 0.6363 (p0) REVERT: A 714 ILE cc_start: 0.8142 (pt) cc_final: 0.7916 (mt) REVERT: A 1504 GLU cc_start: 0.7019 (tp30) cc_final: 0.6803 (tp30) REVERT: A 1593 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7962 (mttm) REVERT: B 124 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7794 (tp) REVERT: B 137 ARG cc_start: 0.6983 (tpp-160) cc_final: 0.6610 (tpp-160) REVERT: B 144 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7720 (mtmt) REVERT: B 318 ASP cc_start: 0.8255 (t70) cc_final: 0.8017 (t70) REVERT: B 472 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7424 (pp) REVERT: B 618 LYS cc_start: 0.8558 (mptt) cc_final: 0.8228 (mmmm) REVERT: B 663 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8408 (ttpp) REVERT: B 686 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7341 (mt-10) outliers start: 57 outliers final: 25 residues processed: 398 average time/residue: 1.4101 time to fit residues: 622.5235 Evaluate side-chains 385 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 355 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS 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 415 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 518 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 691 LEU 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 1489 ILE Chi-restraints excluded: chain A residue 1561 LYS Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1672 LEU 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 188 ILE 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 628 GLU Chi-restraints excluded: chain B residue 652 ILE 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 106 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 121 optimal weight: 0.0570 chunk 93 optimal weight: 0.0470 chunk 133 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 A 984 HIS A1506 ASN A1568 HIS B 210 HIS B 513 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.103785 restraints weight = 22736.059| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.96 r_work: 0.3165 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17027 Z= 0.125 Angle : 0.571 10.012 23118 Z= 0.293 Chirality : 0.042 0.261 2493 Planarity : 0.005 0.060 2854 Dihedral : 15.267 174.129 2665 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 3.20 % Allowed : 24.93 % Favored : 71.87 % 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: 0.04 (0.19), residues: 1953 helix: 1.89 (0.20), residues: 689 sheet: 0.21 (0.31), residues: 262 loop : -1.44 (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 0.021 0.001 PHE A1570 TYR 0.019 0.001 TYR A 149 ARG 0.006 0.000 ARG A 738 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 625) hydrogen bonds : angle 3.97227 ( 1854) metal coordination : bond 0.00398 ( 16) metal coordination : angle 3.31187 ( 21) covalent geometry : bond 0.00289 (17011) covalent geometry : angle 0.56260 (23097) *********************** 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 426 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 371 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8461 (mtpt) REVERT: A 174 SER cc_start: 0.8634 (t) cc_final: 0.8288 (p) REVERT: A 236 ARG cc_start: 0.8339 (ttm170) cc_final: 0.8104 (ttm170) REVERT: A 511 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8397 (mtt180) REVERT: A 628 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.8248 (mtm110) REVERT: A 656 GLU cc_start: 0.7697 (pm20) cc_final: 0.7484 (pm20) REVERT: A 659 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6919 (t80) REVERT: A 663 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7288 (mt-10) REVERT: A 696 ASN cc_start: 0.6707 (p0) cc_final: 0.6409 (p0) REVERT: A 945 PHE cc_start: 0.8303 (m-80) cc_final: 0.8038 (m-80) REVERT: A 1489 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7587 (mt) REVERT: A 1504 GLU cc_start: 0.7050 (tp30) cc_final: 0.6836 (tp30) REVERT: A 1592 ASN cc_start: 0.8041 (m-40) cc_final: 0.7733 (m110) REVERT: A 1596 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7400 (mp10) REVERT: B 124 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7836 (tp) REVERT: B 137 ARG cc_start: 0.6955 (tpp-160) cc_final: 0.6718 (tpp-160) REVERT: B 144 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7663 (mtmt) REVERT: B 318 ASP cc_start: 0.8251 (t70) cc_final: 0.8036 (t70) REVERT: B 472 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7378 (pp) REVERT: B 497 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7693 (mt) REVERT: B 566 SER cc_start: 0.7806 (OUTLIER) cc_final: 0.7146 (p) REVERT: B 618 LYS cc_start: 0.8549 (mptt) cc_final: 0.8225 (mmmm) REVERT: B 663 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8406 (ttpp) REVERT: B 686 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7279 (mt-10) outliers start: 55 outliers final: 24 residues processed: 401 average time/residue: 1.4030 time to fit residues: 619.6004 Evaluate side-chains 389 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 356 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 221 LEU 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 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 518 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 659 PHE 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 1561 LYS 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 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 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 104 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 128 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.0000 chunk 53 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS A 350 ASN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 ASN A1506 ASN B 194 ASN B 210 HIS B 513 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104562 restraints weight = 22514.866| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.95 r_work: 0.3180 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17027 Z= 0.117 Angle : 0.560 9.361 23118 Z= 0.288 Chirality : 0.042 0.243 2493 Planarity : 0.004 0.065 2854 Dihedral : 15.209 173.842 2665 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 3.44 % Allowed : 25.80 % 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: 0.22 (0.19), residues: 1953 helix: 2.06 (0.20), residues: 688 sheet: 0.25 (0.31), residues: 262 loop : -1.32 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 612 HIS 0.008 0.001 HIS A 328 PHE 0.021 0.001 PHE A1570 TYR 0.015 0.001 TYR A 149 ARG 0.007 0.000 ARG A 738 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 625) hydrogen bonds : angle 3.90171 ( 1854) metal coordination : bond 0.00342 ( 16) metal coordination : angle 3.18110 ( 21) covalent geometry : bond 0.00266 (17011) covalent geometry : angle 0.55248 (23097) *********************** 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 412 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 353 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8480 (mtpt) REVERT: A 174 SER cc_start: 0.8633 (t) cc_final: 0.8281 (p) REVERT: A 236 ARG cc_start: 0.8303 (ttm170) cc_final: 0.8089 (ttm170) REVERT: A 415 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: A 511 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8376 (mtt180) REVERT: A 627 MET cc_start: 0.8539 (mmm) cc_final: 0.7793 (mmm) REVERT: A 628 ARG cc_start: 0.8641 (mtm-85) cc_final: 0.8277 (mtm110) REVERT: A 659 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6849 (t80) REVERT: A 663 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7288 (mt-10) REVERT: A 696 ASN cc_start: 0.6724 (p0) cc_final: 0.6401 (p0) REVERT: A 697 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7281 (mtm-85) REVERT: A 1593 LYS cc_start: 0.8316 (ttmt) cc_final: 0.8092 (mttt) REVERT: A 1596 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8170 (mm110) REVERT: B 32 PHE cc_start: 0.7740 (m-80) cc_final: 0.7528 (m-80) REVERT: B 124 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7853 (tp) REVERT: B 137 ARG cc_start: 0.6950 (tpp-160) cc_final: 0.6695 (tpp-160) REVERT: B 144 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7649 (mtmt) REVERT: B 263 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7643 (ttm-80) REVERT: B 318 ASP cc_start: 0.8217 (t70) cc_final: 0.7993 (t70) REVERT: B 472 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7322 (pp) REVERT: B 497 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7666 (mt) REVERT: B 566 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7102 (p) REVERT: B 595 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8031 (mtm180) REVERT: B 618 LYS cc_start: 0.8556 (mptt) cc_final: 0.8226 (mmmm) REVERT: B 663 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8381 (ttpp) REVERT: B 686 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7247 (mt-10) outliers start: 59 outliers final: 28 residues processed: 384 average time/residue: 1.4393 time to fit residues: 609.4570 Evaluate side-chains 389 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 350 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 308 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 415 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 518 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 697 ARG 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 1561 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 148 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 ASN A1506 ASN A1592 ASN B 210 HIS B 513 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.117378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100133 restraints weight = 22518.239| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.92 r_work: 0.3104 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17027 Z= 0.250 Angle : 0.702 11.124 23118 Z= 0.360 Chirality : 0.049 0.319 2493 Planarity : 0.006 0.068 2854 Dihedral : 15.510 174.284 2665 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.96 % Rotamer: Outliers : 3.90 % Allowed : 26.03 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.27 % 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: -0.07 (0.18), residues: 1953 helix: 1.71 (0.20), residues: 695 sheet: 0.42 (0.31), residues: 255 loop : -1.53 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 556 HIS 0.010 0.002 HIS A 328 PHE 0.022 0.002 PHE A1570 TYR 0.028 0.002 TYR A 149 ARG 0.004 0.001 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.06006 ( 625) hydrogen bonds : angle 4.28970 ( 1854) metal coordination : bond 0.00799 ( 16) metal coordination : angle 3.89505 ( 21) covalent geometry : bond 0.00620 (17011) covalent geometry : angle 0.69278 (23097) *********************** 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 455 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 388 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: A 55 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8581 (mtpt) REVERT: A 174 SER cc_start: 0.8709 (t) cc_final: 0.8375 (p) REVERT: A 236 ARG cc_start: 0.8319 (ttm170) cc_final: 0.8096 (ttm170) REVERT: A 288 ASP cc_start: 0.7654 (t0) cc_final: 0.7410 (t0) REVERT: A 308 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: A 415 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: A 511 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8364 (mtt180) REVERT: A 627 MET cc_start: 0.8631 (mmm) cc_final: 0.7936 (mmm) REVERT: A 639 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7019 (tm-30) REVERT: A 1496 GLU cc_start: 0.7605 (tp30) cc_final: 0.7387 (mp0) REVERT: A 1499 GLU cc_start: 0.6719 (mp0) cc_final: 0.6515 (mp0) REVERT: A 1596 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8215 (mm110) REVERT: B 124 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7948 (tp) REVERT: B 144 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7746 (mtmt) REVERT: B 222 SER cc_start: 0.8613 (t) cc_final: 0.8313 (p) REVERT: B 472 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7634 (pp) REVERT: B 566 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7588 (p) REVERT: B 595 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8057 (mtm180) REVERT: B 663 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8400 (ttpp) outliers start: 67 outliers final: 32 residues processed: 418 average time/residue: 1.4100 time to fit residues: 650.3504 Evaluate side-chains 419 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 377 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU 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 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 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 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 556 THR Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1561 LYS Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1631 VAL 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 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 652 ILE Chi-restraints excluded: chain B residue 664 VAL 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 182 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 A1506 ASN B 194 ASN B 210 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100921 restraints weight = 22376.842| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.90 r_work: 0.3116 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17027 Z= 0.206 Angle : 0.659 10.043 23118 Z= 0.339 Chirality : 0.046 0.247 2493 Planarity : 0.005 0.074 2854 Dihedral : 15.508 174.671 2665 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 3.90 % Allowed : 26.91 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.27 % 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: -0.00 (0.19), residues: 1953 helix: 1.81 (0.20), residues: 689 sheet: 0.46 (0.31), residues: 265 loop : -1.52 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 556 HIS 0.009 0.002 HIS A 328 PHE 0.023 0.002 PHE A1570 TYR 0.025 0.002 TYR A 149 ARG 0.004 0.000 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.05276 ( 625) hydrogen bonds : angle 4.22198 ( 1854) metal coordination : bond 0.00665 ( 16) metal coordination : angle 3.48111 ( 21) covalent geometry : bond 0.00508 (17011) covalent geometry : angle 0.65106 (23097) *********************** 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 441 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 374 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: A 55 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8536 (mtpt) REVERT: A 174 SER cc_start: 0.8685 (t) cc_final: 0.8359 (p) REVERT: A 236 ARG cc_start: 0.8301 (ttm170) cc_final: 0.8083 (ttm170) REVERT: A 288 ASP cc_start: 0.7745 (t0) cc_final: 0.7458 (t0) REVERT: A 415 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: A 511 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8386 (mtt180) REVERT: A 627 MET cc_start: 0.8607 (mmm) cc_final: 0.7885 (mmm) REVERT: A 639 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7011 (tm-30) REVERT: A 668 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: A 1496 GLU cc_start: 0.7610 (tp30) cc_final: 0.7377 (mp0) REVERT: A 1596 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8180 (mm110) REVERT: B 124 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7940 (tp) REVERT: B 144 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7737 (mtmt) REVERT: B 222 SER cc_start: 0.8572 (t) cc_final: 0.8288 (p) REVERT: B 472 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7684 (pp) REVERT: B 566 SER cc_start: 0.8089 (OUTLIER) cc_final: 0.7549 (p) REVERT: B 595 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8048 (mtm180) REVERT: B 663 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8441 (ttpp) outliers start: 67 outliers final: 32 residues processed: 414 average time/residue: 1.4011 time to fit residues: 640.8542 Evaluate side-chains 415 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 373 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU 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 291 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 ILE 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 516 ASP Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 556 THR 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 782 LYS Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1561 LYS 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 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 652 ILE Chi-restraints excluded: chain B residue 664 VAL 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 111 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 13 optimal weight: 0.0020 chunk 123 optimal weight: 0.0000 chunk 128 optimal weight: 2.9990 chunk 117 optimal weight: 0.0770 chunk 108 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 overall best weight: 0.1728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 306 HIS A 328 HIS A 673 GLN ** A 727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN A1547 HIS B 210 HIS B 281 HIS B 513 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106351 restraints weight = 22598.929| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.93 r_work: 0.3211 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17027 Z= 0.106 Angle : 0.563 8.378 23118 Z= 0.293 Chirality : 0.041 0.237 2493 Planarity : 0.004 0.070 2854 Dihedral : 15.243 174.821 2665 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Rotamer: Outliers : 2.10 % Allowed : 28.77 % Favored : 69.13 % 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: 0.29 (0.19), residues: 1953 helix: 2.12 (0.20), residues: 697 sheet: 0.25 (0.31), residues: 271 loop : -1.33 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 612 HIS 0.008 0.001 HIS A 328 PHE 0.019 0.001 PHE A1570 TYR 0.015 0.001 TYR B 704 ARG 0.004 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 625) hydrogen bonds : angle 3.84260 ( 1854) metal coordination : bond 0.00276 ( 16) metal coordination : angle 2.94975 ( 21) covalent geometry : bond 0.00226 (17011) covalent geometry : angle 0.55583 (23097) *********************** 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 397 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 361 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: A 55 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8432 (mtpt) REVERT: A 143 HIS cc_start: 0.7910 (t-90) cc_final: 0.7695 (t70) REVERT: A 174 SER cc_start: 0.8589 (t) cc_final: 0.8279 (p) REVERT: A 288 ASP cc_start: 0.7463 (t0) cc_final: 0.7244 (t0) REVERT: A 627 MET cc_start: 0.8532 (mmm) cc_final: 0.7859 (mmm) REVERT: A 668 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: A 1459 LEU cc_start: 0.7532 (mt) cc_final: 0.7276 (mp) REVERT: A 1472 GLU cc_start: 0.7047 (mp0) cc_final: 0.6716 (mp0) REVERT: A 1496 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: A 1596 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8151 (mm110) REVERT: A 1647 VAL cc_start: 0.8726 (p) cc_final: 0.8485 (t) REVERT: B 25 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7388 (mm-30) REVERT: B 102 GLU cc_start: 0.7606 (tp30) cc_final: 0.7100 (tp30) REVERT: B 137 ARG cc_start: 0.7049 (tpp-160) cc_final: 0.6781 (tpp-160) REVERT: B 144 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7645 (mtmt) REVERT: B 472 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7448 (pp) REVERT: B 566 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7289 (p) REVERT: B 663 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8377 (ttpp) outliers start: 36 outliers final: 16 residues processed: 383 average time/residue: 1.5805 time to fit residues: 667.8519 Evaluate side-chains 375 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 352 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU 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 320 LYS Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 668 GLN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1561 LYS Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain B residue 64 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 77 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 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 A 905 HIS A1506 ASN ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 513 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102640 restraints weight = 22575.895| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.93 r_work: 0.3150 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17027 Z= 0.157 Angle : 0.624 11.980 23118 Z= 0.320 Chirality : 0.044 0.241 2493 Planarity : 0.005 0.070 2854 Dihedral : 15.326 173.906 2665 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 1.92 % Allowed : 29.24 % Favored : 68.84 % 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: 0.28 (0.19), residues: 1953 helix: 2.08 (0.20), residues: 700 sheet: 0.35 (0.31), residues: 268 loop : -1.35 (0.18), residues: 985 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 0.023 0.002 PHE A1570 TYR 0.020 0.001 TYR A 149 ARG 0.008 0.000 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 625) hydrogen bonds : angle 3.97442 ( 1854) metal coordination : bond 0.00478 ( 16) metal coordination : angle 3.12759 ( 21) covalent geometry : bond 0.00378 (17011) covalent geometry : angle 0.61719 (23097) ********************** 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 401 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 368 time to evaluate : 2.161 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: A 55 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8529 (mtpt) REVERT: A 174 SER cc_start: 0.8651 (t) cc_final: 0.8351 (p) REVERT: A 288 ASP cc_start: 0.7593 (t0) cc_final: 0.7336 (t0) REVERT: A 494 SER cc_start: 0.8483 (p) cc_final: 0.8251 (m) REVERT: A 627 MET cc_start: 0.8568 (mmm) cc_final: 0.7883 (mmm) REVERT: A 739 THR cc_start: 0.8653 (m) cc_final: 0.8414 (p) REVERT: A 1459 LEU cc_start: 0.7568 (mt) cc_final: 0.7367 (mp) REVERT: A 1470 ASP cc_start: 0.7511 (p0) cc_final: 0.7287 (m-30) REVERT: A 1472 GLU cc_start: 0.7154 (mp0) cc_final: 0.6770 (mp0) REVERT: A 1496 GLU cc_start: 0.7448 (tp30) cc_final: 0.7240 (mp0) REVERT: A 1596 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8158 (mm110) REVERT: B 25 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7432 (mm-30) REVERT: B 102 GLU cc_start: 0.7630 (tp30) cc_final: 0.7143 (tp30) REVERT: B 144 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7670 (mtmt) REVERT: B 205 ILE cc_start: 0.7659 (mm) cc_final: 0.7429 (mt) REVERT: B 472 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7420 (pp) REVERT: B 562 LYS cc_start: 0.7346 (ptpt) cc_final: 0.7103 (ptpt) REVERT: B 566 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7363 (p) REVERT: B 595 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8060 (mtm180) outliers start: 33 outliers final: 19 residues processed: 384 average time/residue: 1.5532 time to fit residues: 656.8987 Evaluate side-chains 387 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 362 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU 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 320 LYS Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 516 ASP 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 1449 ASN Chi-restraints excluded: chain A residue 1561 LYS Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain B residue 64 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 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 697 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 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 ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 513 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.120827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103746 restraints weight = 22610.411| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.93 r_work: 0.3163 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17027 Z= 0.123 Angle : 0.592 11.583 23118 Z= 0.303 Chirality : 0.042 0.238 2493 Planarity : 0.005 0.070 2854 Dihedral : 15.291 173.890 2665 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 1.69 % Allowed : 29.64 % Favored : 68.67 % 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: 0.36 (0.19), residues: 1953 helix: 2.19 (0.20), residues: 695 sheet: 0.36 (0.31), residues: 268 loop : -1.31 (0.18), residues: 990 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 0.022 0.001 PHE A1570 TYR 0.015 0.001 TYR A 149 ARG 0.007 0.000 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 625) hydrogen bonds : angle 3.90611 ( 1854) metal coordination : bond 0.00311 ( 16) metal coordination : angle 3.01203 ( 21) covalent geometry : bond 0.00285 (17011) covalent geometry : angle 0.58482 (23097) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15970.68 seconds wall clock time: 276 minutes 59.41 seconds (16619.41 seconds total)