Starting phenix.real_space_refine on Sun Dec 29 18:59:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xso_33429/12_2024/7xso_33429.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xso_33429/12_2024/7xso_33429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xso_33429/12_2024/7xso_33429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xso_33429/12_2024/7xso_33429.map" model { file = "/net/cci-nas-00/data/ceres_data/7xso_33429/12_2024/7xso_33429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xso_33429/12_2024/7xso_33429.cif" } resolution = 3.01 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= 0.004 sd= 0.047 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 35 5.49 5 S 33 5.16 5 C 6836 2.51 5 N 1913 2.21 5 O 2150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10971 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1271, 10232 Classifications: {'peptide': 1271} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 60, 'TRANS': 1210} Chain breaks: 5 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 18, 'rna3p': 16} 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 77.755 24.345 20.422 1.00 56.77 S ATOM 947 SG CYS A 121 81.150 23.663 18.457 1.00 61.88 S ATOM 993 SG CYS A 127 80.468 27.509 19.938 1.00 55.76 S ATOM 1017 SG CYS A 130 81.117 24.681 22.142 1.00 54.16 S ATOM 3605 SG CYS A 491 55.617 30.294 46.468 1.00 54.94 S ATOM 3673 SG CYS A 501 56.577 28.803 43.330 1.00 54.99 S ATOM 3687 SG CYS A 503 54.317 32.071 42.736 1.00 54.55 S ATOM 3709 SG CYS A 506 57.891 32.628 43.859 1.00 50.92 S ATOM 5680 SG CYS A 750 41.443 35.171 73.361 1.00 67.60 S ATOM 5693 SG CYS A 752 39.561 38.582 72.519 1.00 60.45 S ATOM 5715 SG CYS A 755 43.237 38.815 71.688 1.00 54.67 S ATOM 7689 SG CYS A1018 41.329 59.400 103.367 1.00 44.86 S ATOM 7914 SG CYS A1406 42.342 55.852 102.186 1.00 50.92 S ATOM 7965 SG CYS A1414 38.269 57.860 101.887 1.00 45.70 S ATOM 7982 SG CYS A1417 41.074 58.599 99.691 1.00 42.97 S Time building chain proxies: 6.40, per 1000 atoms: 0.58 Number of scatterers: 10971 At special positions: 0 Unit cell: (111.15, 115.425, 140.22, 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 33 16.00 P 35 15.00 O 2150 8.00 N 1913 7.00 C 6836 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: 2.91 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 88 " 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 506 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " 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 A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " Number of angles added : 21 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2324 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 17 sheets defined 29.0% alpha, 22.5% beta 0 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.570A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.605A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 214 through 224 removed outlier: 4.166A pdb=" N LEU A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 287 removed outlier: 3.848A pdb=" N ASN A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.226A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 removed outlier: 5.788A 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 348 Processing helix chain 'A' and resid 354 through 375 removed outlier: 3.554A pdb=" N PHE A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 569 through 580 removed outlier: 3.526A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 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 637 removed outlier: 3.952A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 658 removed outlier: 3.530A pdb=" N CYS A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.560A 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 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 723 through 739 removed outlier: 3.627A pdb=" N HIS A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 3.968A 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 881 removed outlier: 3.523A pdb=" N LYS A 877 " --> pdb=" O PRO A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.813A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 removed outlier: 3.848A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.816A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A1493 " --> pdb=" O ILE A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1499 Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.540A pdb=" N ASP A1540 " --> pdb=" O LEU A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1603 Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.600A 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.699A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA A 53 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP A 195 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 13.588A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 192 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.966A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.182A 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: 6.184A 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 512 through 514 removed outlier: 6.616A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY A 600 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.616A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.788A pdb=" N VAL A 432 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AB1, first strand: chain 'A' and resid 533 through 534 removed outlier: 3.804A pdb=" N THR A 539 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.777A pdb=" N ARG A 719 " --> pdb=" O LYS A 704 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.777A pdb=" N ARG A 719 " --> pdb=" O LYS A 704 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB5, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB6, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.562A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.562A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 957 " --> pdb=" O ILE A1564 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE A1564 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU A 959 " --> pdb=" O ILE A1562 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE A1562 " --> pdb=" O GLU A 959 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.555A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 4.95 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1766 1.28 - 1.41: 2987 1.41 - 1.54: 6409 1.54 - 1.68: 85 1.68 - 1.81: 45 Bond restraints: 11292 Sorted by residual: bond pdb=" C PRO A1687 " pdb=" O PRO A1687 " ideal model delta sigma weight residual 1.233 1.149 0.084 1.16e-02 7.43e+03 5.20e+01 bond pdb=" O3' C D 15 " pdb=" P G D 16 " ideal model delta sigma weight residual 1.607 1.500 0.107 1.50e-02 4.44e+03 5.13e+01 bond pdb=" C PRO A1690 " pdb=" O PRO A1690 " ideal model delta sigma weight residual 1.235 1.183 0.052 7.90e-03 1.60e+04 4.40e+01 bond pdb=" O3' U D -2 " pdb=" P A D -1 " ideal model delta sigma weight residual 1.607 1.517 0.090 1.50e-02 4.44e+03 3.63e+01 bond pdb=" C PRO A1684 " pdb=" O PRO A1684 " ideal model delta sigma weight residual 1.234 1.169 0.065 1.14e-02 7.69e+03 3.22e+01 ... (remaining 11287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 15146 3.42 - 6.83: 221 6.83 - 10.25: 23 10.25 - 13.66: 0 13.66 - 17.08: 1 Bond angle restraints: 15391 Sorted by residual: angle pdb=" N PRO A1690 " pdb=" CA PRO A1690 " pdb=" C PRO A1690 " ideal model delta sigma weight residual 110.74 93.66 17.08 1.66e+00 3.63e-01 1.06e+02 angle pdb=" N LEU A 975 " pdb=" CA LEU A 975 " pdb=" C LEU A 975 " ideal model delta sigma weight residual 113.30 103.67 9.63 1.34e+00 5.57e-01 5.17e+01 angle pdb=" O3' C D -7 " pdb=" C3' C D -7 " pdb=" C2' C D -7 " ideal model delta sigma weight residual 113.70 104.35 9.35 1.50e+00 4.44e-01 3.89e+01 angle pdb=" O2' C D -7 " pdb=" C2' C D -7 " pdb=" C1' C D -7 " ideal model delta sigma weight residual 108.40 99.06 9.34 1.50e+00 4.44e-01 3.87e+01 angle pdb=" O4' A D -1 " pdb=" C1' A D -1 " pdb=" C2' A D -1 " ideal model delta sigma weight residual 105.80 100.12 5.68 1.00e+00 1.00e+00 3.22e+01 ... (remaining 15386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 6534 35.24 - 70.47: 261 70.47 - 105.71: 19 105.71 - 140.95: 0 140.95 - 176.18: 9 Dihedral angle restraints: 6823 sinusoidal: 3192 harmonic: 3631 Sorted by residual: dihedral pdb=" O4' U D -13 " pdb=" C1' U D -13 " pdb=" N1 U D -13 " pdb=" C2 U D -13 " ideal model delta sinusoidal sigma weight residual -160.00 16.18 -176.18 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U D -10 " pdb=" C1' U D -10 " pdb=" N1 U D -10 " pdb=" C2 U D -10 " ideal model delta sinusoidal sigma weight residual 200.00 32.16 167.84 1 1.50e+01 4.44e-03 8.44e+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 41.91 158.09 1 1.50e+01 4.44e-03 8.23e+01 ... (remaining 6820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1441 0.092 - 0.185: 182 0.185 - 0.277: 24 0.277 - 0.369: 5 0.369 - 0.461: 1 Chirality restraints: 1653 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 2.05 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" C1' U D -13 " pdb=" O4' U D -13 " pdb=" C2' U D -13 " pdb=" N1 U D -13 " both_signs ideal model delta sigma weight residual False 2.47 2.10 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA PRO A1690 " pdb=" N PRO A1690 " pdb=" C PRO A1690 " pdb=" CB PRO A1690 " both_signs ideal model delta sigma weight residual False 2.72 3.05 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 1650 not shown) Planarity restraints: 1868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 391 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C SER A 391 " 0.064 2.00e-02 2.50e+03 pdb=" O SER A 391 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS A 392 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D -1 " 0.047 2.00e-02 2.50e+03 2.19e-02 1.31e+01 pdb=" N9 A D -1 " -0.050 2.00e-02 2.50e+03 pdb=" C8 A D -1 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A D -1 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A D -1 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A D -1 " 0.010 2.00e-02 2.50e+03 pdb=" N6 A D -1 " 0.003 2.00e-02 2.50e+03 pdb=" N1 A D -1 " 0.014 2.00e-02 2.50e+03 pdb=" C2 A D -1 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A D -1 " -0.013 2.00e-02 2.50e+03 pdb=" C4 A D -1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 972 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLU A 972 " -0.058 2.00e-02 2.50e+03 pdb=" O GLU A 972 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN A 973 " 0.020 2.00e-02 2.50e+03 ... (remaining 1865 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 501 2.71 - 3.25: 9439 3.25 - 3.80: 16900 3.80 - 4.35: 21160 4.35 - 4.90: 36860 Nonbonded interactions: 84860 Sorted by model distance: nonbonded pdb=" O SER A 438 " pdb=" OG SER A 438 " model vdw 2.157 3.040 nonbonded pdb=" O THR A 751 " pdb=" OG1 THR A 751 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR A1645 " pdb=" OP1 C D 14 " model vdw 2.327 3.040 nonbonded pdb=" OG SER A 813 " pdb=" OE1 GLU A 995 " model vdw 2.330 3.040 nonbonded pdb=" OD1 ASN A1448 " pdb=" NH1 ARG A1498 " model vdw 2.338 3.120 ... (remaining 84855 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.150 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.107 11292 Z= 0.598 Angle : 1.020 17.076 15391 Z= 0.614 Chirality : 0.066 0.461 1653 Planarity : 0.008 0.082 1868 Dihedral : 18.965 176.183 4499 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 3.99 % Allowed : 14.60 % Favored : 81.41 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.19), residues: 1259 helix: -2.12 (0.21), residues: 321 sheet: -0.33 (0.34), residues: 208 loop : -2.49 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A1685 HIS 0.009 0.002 HIS A 924 PHE 0.023 0.003 PHE A 192 TYR 0.019 0.002 TYR A 860 ARG 0.008 0.001 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.5940 (m-30) REVERT: A 51 ARG cc_start: 0.8520 (ptp-170) cc_final: 0.8279 (mtp-110) REVERT: A 73 GLU cc_start: 0.7227 (tt0) cc_final: 0.6854 (mt-10) REVERT: A 142 VAL cc_start: 0.8871 (t) cc_final: 0.8487 (p) REVERT: A 287 ASN cc_start: 0.8153 (m110) cc_final: 0.7895 (m110) REVERT: A 291 GLU cc_start: 0.7169 (tp30) cc_final: 0.6959 (tp30) REVERT: A 293 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7573 (tp) REVERT: A 318 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.6242 (p0) REVERT: A 334 VAL cc_start: 0.8029 (t) cc_final: 0.7756 (m) REVERT: A 401 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8137 (tp) REVERT: A 509 MET cc_start: 0.8247 (mmm) cc_final: 0.7419 (mmm) REVERT: A 567 LYS cc_start: 0.8244 (ptmt) cc_final: 0.8023 (ptmm) REVERT: A 581 GLU cc_start: 0.6926 (pp20) cc_final: 0.6581 (pp20) REVERT: A 623 LYS cc_start: 0.8259 (ttmt) cc_final: 0.8022 (ttpp) REVERT: A 646 LEU cc_start: 0.7862 (tp) cc_final: 0.7661 (tp) REVERT: A 651 PHE cc_start: 0.8274 (m-80) cc_final: 0.7820 (m-80) REVERT: A 653 GLU cc_start: 0.6614 (mp0) cc_final: 0.6309 (mp0) REVERT: A 689 SER cc_start: 0.8436 (m) cc_final: 0.8037 (t) REVERT: A 778 ASN cc_start: 0.8190 (p0) cc_final: 0.7956 (p0) REVERT: A 847 ASP cc_start: 0.7148 (m-30) cc_final: 0.6917 (m-30) REVERT: A 944 GLU cc_start: 0.7397 (pm20) cc_final: 0.7042 (pm20) REVERT: A 1488 ARG cc_start: 0.7780 (mtt-85) cc_final: 0.7398 (mtt180) REVERT: A 1489 ILE cc_start: 0.8124 (pt) cc_final: 0.7875 (mp) REVERT: A 1493 LYS cc_start: 0.8230 (ptpp) cc_final: 0.7988 (pttp) REVERT: A 1497 ILE cc_start: 0.8047 (mm) cc_final: 0.7815 (mt) REVERT: A 1570 PHE cc_start: 0.7920 (p90) cc_final: 0.7340 (p90) outliers start: 44 outliers final: 18 residues processed: 299 average time/residue: 0.3245 time to fit residues: 128.2731 Evaluate side-chains 238 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1653 LYS Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1679 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN A 708 ASN A 871 ASN A 901 ASN A1537 GLN A1544 ASN A1604 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11292 Z= 0.192 Angle : 0.588 7.677 15391 Z= 0.309 Chirality : 0.044 0.262 1653 Planarity : 0.006 0.063 1868 Dihedral : 18.316 175.917 1963 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.81 % Allowed : 19.13 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.21), residues: 1259 helix: -0.08 (0.28), residues: 328 sheet: -0.09 (0.35), residues: 201 loop : -1.95 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 612 HIS 0.004 0.001 HIS A 789 PHE 0.017 0.001 PHE A 546 TYR 0.019 0.001 TYR A 808 ARG 0.007 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6539 (OUTLIER) cc_final: 0.5945 (m-30) REVERT: A 52 THR cc_start: 0.8465 (p) cc_final: 0.8235 (t) REVERT: A 287 ASN cc_start: 0.8015 (m110) cc_final: 0.7751 (m110) REVERT: A 334 VAL cc_start: 0.8059 (t) cc_final: 0.7798 (m) REVERT: A 509 MET cc_start: 0.8310 (mmm) cc_final: 0.7287 (mmm) REVERT: A 545 LEU cc_start: 0.8461 (tt) cc_final: 0.8244 (tp) REVERT: A 567 LYS cc_start: 0.8290 (ptmt) cc_final: 0.8047 (ptmm) REVERT: A 623 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7978 (ttpp) REVERT: A 651 PHE cc_start: 0.8281 (m-80) cc_final: 0.7815 (m-80) REVERT: A 653 GLU cc_start: 0.6753 (mp0) cc_final: 0.6427 (mp0) REVERT: A 689 SER cc_start: 0.8175 (m) cc_final: 0.7953 (p) REVERT: A 705 ARG cc_start: 0.8276 (mtp85) cc_final: 0.8060 (mtp-110) REVERT: A 821 LYS cc_start: 0.8088 (tttt) cc_final: 0.7818 (tttp) REVERT: A 847 ASP cc_start: 0.7001 (m-30) cc_final: 0.6789 (m-30) REVERT: A 944 GLU cc_start: 0.7344 (pm20) cc_final: 0.6972 (pm20) REVERT: A 977 LEU cc_start: 0.8144 (mt) cc_final: 0.7935 (mp) REVERT: A 1401 LYS cc_start: 0.7896 (tttt) cc_final: 0.7617 (tptt) REVERT: A 1497 ILE cc_start: 0.8038 (mm) cc_final: 0.7780 (mt) REVERT: A 1570 PHE cc_start: 0.8069 (p90) cc_final: 0.7520 (p90) outliers start: 31 outliers final: 15 residues processed: 244 average time/residue: 0.3258 time to fit residues: 104.6900 Evaluate side-chains 231 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1653 LYS Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 105 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 40 optimal weight: 0.0570 chunk 94 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 993 ASN A1449 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11292 Z= 0.152 Angle : 0.531 6.979 15391 Z= 0.277 Chirality : 0.042 0.224 1653 Planarity : 0.005 0.060 1868 Dihedral : 17.979 179.086 1937 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.27 % Allowed : 19.85 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1259 helix: 0.72 (0.29), residues: 329 sheet: 0.11 (0.36), residues: 192 loop : -1.62 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 PHE 0.014 0.001 PHE A 824 TYR 0.012 0.001 TYR A1663 ARG 0.004 0.000 ARG A 738 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7108 (tp30) cc_final: 0.6594 (tp30) REVERT: A 51 ARG cc_start: 0.8463 (ptp-170) cc_final: 0.8196 (mtp-110) REVERT: A 206 THR cc_start: 0.8478 (t) cc_final: 0.8000 (m) REVERT: A 229 LYS cc_start: 0.8316 (ttmm) cc_final: 0.8045 (mtpt) REVERT: A 287 ASN cc_start: 0.7931 (m110) cc_final: 0.7702 (m110) REVERT: A 401 LEU cc_start: 0.8406 (mm) cc_final: 0.8189 (mt) REVERT: A 417 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8445 (tt) REVERT: A 509 MET cc_start: 0.8315 (mmm) cc_final: 0.7288 (mmm) REVERT: A 623 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7989 (ttpp) REVERT: A 651 PHE cc_start: 0.8292 (m-80) cc_final: 0.7886 (m-80) REVERT: A 653 GLU cc_start: 0.6808 (mp0) cc_final: 0.6464 (mp0) REVERT: A 689 SER cc_start: 0.8166 (m) cc_final: 0.7944 (p) REVERT: A 719 ARG cc_start: 0.7967 (mmt90) cc_final: 0.7510 (mmt90) REVERT: A 763 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7015 (tt0) REVERT: A 808 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.6948 (m-80) REVERT: A 944 GLU cc_start: 0.7315 (pm20) cc_final: 0.6911 (pm20) REVERT: A 1401 LYS cc_start: 0.7955 (tttt) cc_final: 0.7680 (tptt) REVERT: A 1489 ILE cc_start: 0.8115 (pt) cc_final: 0.7910 (mm) REVERT: A 1493 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7938 (pttp) REVERT: A 1497 ILE cc_start: 0.8090 (mm) cc_final: 0.7875 (mt) REVERT: A 1570 PHE cc_start: 0.8158 (p90) cc_final: 0.7595 (p90) outliers start: 25 outliers final: 16 residues processed: 240 average time/residue: 0.3272 time to fit residues: 104.9961 Evaluate side-chains 234 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 1493 LYS Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 0.0970 chunk 88 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 498 GLN A 502 ASN A1449 ASN A1596 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11292 Z= 0.169 Angle : 0.530 7.167 15391 Z= 0.275 Chirality : 0.043 0.228 1653 Planarity : 0.005 0.060 1868 Dihedral : 17.923 178.992 1930 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.35 % Allowed : 19.58 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1259 helix: 1.22 (0.29), residues: 324 sheet: 0.29 (0.36), residues: 203 loop : -1.50 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 PHE 0.015 0.001 PHE A 824 TYR 0.011 0.001 TYR A 808 ARG 0.004 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.6077 (m-30) REVERT: A 51 ARG cc_start: 0.8442 (ptp-170) cc_final: 0.8160 (mtp-110) REVERT: A 287 ASN cc_start: 0.7900 (m110) cc_final: 0.7634 (m110) REVERT: A 401 LEU cc_start: 0.8409 (mm) cc_final: 0.8204 (mt) REVERT: A 653 GLU cc_start: 0.6832 (mp0) cc_final: 0.6487 (mp0) REVERT: A 719 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7520 (mmt90) REVERT: A 748 GLU cc_start: 0.7468 (pp20) cc_final: 0.7088 (pp20) REVERT: A 763 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: A 944 GLU cc_start: 0.7278 (pm20) cc_final: 0.6894 (pm20) REVERT: A 1401 LYS cc_start: 0.8000 (tttt) cc_final: 0.7735 (tptt) REVERT: A 1493 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7951 (pttp) REVERT: A 1497 ILE cc_start: 0.8201 (mm) cc_final: 0.8001 (mt) REVERT: A 1570 PHE cc_start: 0.8168 (p90) cc_final: 0.7584 (p90) outliers start: 37 outliers final: 23 residues processed: 242 average time/residue: 0.3116 time to fit residues: 101.4164 Evaluate side-chains 240 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS A 455 HIS A1544 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11292 Z= 0.352 Angle : 0.633 9.980 15391 Z= 0.329 Chirality : 0.048 0.254 1653 Planarity : 0.005 0.062 1868 Dihedral : 18.089 179.274 1930 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.72 % Allowed : 19.95 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1259 helix: 0.99 (0.29), residues: 331 sheet: 0.50 (0.36), residues: 192 loop : -1.51 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 612 HIS 0.006 0.001 HIS A 924 PHE 0.017 0.002 PHE A 192 TYR 0.015 0.002 TYR A 860 ARG 0.004 0.000 ARG A 935 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 1.382 Fit side-chains REVERT: A 27 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6108 (m-30) REVERT: A 51 ARG cc_start: 0.8453 (ptp-170) cc_final: 0.8126 (mtp-110) REVERT: A 206 THR cc_start: 0.8634 (t) cc_final: 0.8277 (m) REVERT: A 285 LYS cc_start: 0.7980 (ttmt) cc_final: 0.7774 (ttpp) REVERT: A 287 ASN cc_start: 0.8014 (m110) cc_final: 0.7778 (m110) REVERT: A 522 SER cc_start: 0.8412 (m) cc_final: 0.8049 (p) REVERT: A 546 PHE cc_start: 0.8217 (p90) cc_final: 0.8010 (p90) REVERT: A 653 GLU cc_start: 0.6853 (mp0) cc_final: 0.6505 (mp0) REVERT: A 748 GLU cc_start: 0.7457 (pp20) cc_final: 0.7026 (pp20) REVERT: A 763 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: A 944 GLU cc_start: 0.7328 (pm20) cc_final: 0.6981 (pm20) REVERT: A 1389 LYS cc_start: 0.5336 (mmtm) cc_final: 0.4993 (ttpp) REVERT: A 1401 LYS cc_start: 0.8076 (tttt) cc_final: 0.7824 (tptt) outliers start: 41 outliers final: 33 residues processed: 255 average time/residue: 0.3082 time to fit residues: 104.9163 Evaluate side-chains 256 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 499 ILE 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 636 GLU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1669 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 986 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11292 Z= 0.163 Angle : 0.535 7.457 15391 Z= 0.279 Chirality : 0.043 0.233 1653 Planarity : 0.004 0.059 1868 Dihedral : 17.848 179.312 1930 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.63 % Allowed : 22.21 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1259 helix: 1.60 (0.30), residues: 317 sheet: 0.30 (0.36), residues: 207 loop : -1.36 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 PHE 0.013 0.001 PHE A 824 TYR 0.010 0.001 TYR A 808 ARG 0.004 0.000 ARG A 738 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 1.288 Fit side-chains REVERT: A 51 ARG cc_start: 0.8347 (ptp-170) cc_final: 0.8063 (mtp-110) REVERT: A 72 GLU cc_start: 0.7278 (tt0) cc_final: 0.6980 (tt0) REVERT: A 110 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8310 (m) REVERT: A 170 VAL cc_start: 0.7960 (m) cc_final: 0.7708 (t) REVERT: A 206 THR cc_start: 0.8485 (t) cc_final: 0.8164 (m) REVERT: A 287 ASN cc_start: 0.7839 (m110) cc_final: 0.7597 (m110) REVERT: A 499 ILE cc_start: 0.8414 (mm) cc_final: 0.8071 (mm) REVERT: A 651 PHE cc_start: 0.8364 (m-10) cc_final: 0.8044 (m-80) REVERT: A 653 GLU cc_start: 0.6847 (mp0) cc_final: 0.6506 (mp0) REVERT: A 739 THR cc_start: 0.8445 (m) cc_final: 0.8009 (p) REVERT: A 748 GLU cc_start: 0.7432 (pp20) cc_final: 0.7021 (pp20) REVERT: A 763 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7009 (tt0) REVERT: A 944 GLU cc_start: 0.7227 (pm20) cc_final: 0.6910 (pm20) REVERT: A 1389 LYS cc_start: 0.5261 (mmtm) cc_final: 0.4999 (ttpp) REVERT: A 1401 LYS cc_start: 0.8073 (tttt) cc_final: 0.7818 (tptt) outliers start: 29 outliers final: 25 residues processed: 239 average time/residue: 0.3030 time to fit residues: 96.5376 Evaluate side-chains 246 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 986 ASN A1596 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11292 Z= 0.149 Angle : 0.521 7.839 15391 Z= 0.270 Chirality : 0.042 0.227 1653 Planarity : 0.004 0.059 1868 Dihedral : 17.783 179.356 1930 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.08 % Allowed : 21.76 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1259 helix: 1.75 (0.29), residues: 318 sheet: 0.35 (0.35), residues: 200 loop : -1.27 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 PHE 0.014 0.001 PHE A 546 TYR 0.009 0.001 TYR A1655 ARG 0.003 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 1.327 Fit side-chains REVERT: A 51 ARG cc_start: 0.8345 (ptp-170) cc_final: 0.8059 (mtp-110) REVERT: A 72 GLU cc_start: 0.7282 (tt0) cc_final: 0.7023 (tt0) REVERT: A 206 THR cc_start: 0.8467 (t) cc_final: 0.8095 (m) REVERT: A 287 ASN cc_start: 0.7823 (m110) cc_final: 0.7568 (m110) REVERT: A 509 MET cc_start: 0.8406 (mmm) cc_final: 0.7343 (mmm) REVERT: A 651 PHE cc_start: 0.8359 (m-10) cc_final: 0.8045 (m-80) REVERT: A 653 GLU cc_start: 0.6857 (mp0) cc_final: 0.6512 (mp0) REVERT: A 739 THR cc_start: 0.8455 (m) cc_final: 0.8033 (p) REVERT: A 748 GLU cc_start: 0.7430 (pp20) cc_final: 0.7022 (pp20) REVERT: A 763 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7016 (tt0) REVERT: A 944 GLU cc_start: 0.7239 (pm20) cc_final: 0.6945 (pm20) REVERT: A 1389 LYS cc_start: 0.5263 (mmtm) cc_final: 0.5038 (ttpp) REVERT: A 1401 LYS cc_start: 0.8076 (tttt) cc_final: 0.7814 (tptt) REVERT: A 1570 PHE cc_start: 0.8171 (p90) cc_final: 0.7580 (p90) REVERT: A 1589 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6632 (tm-30) outliers start: 34 outliers final: 23 residues processed: 247 average time/residue: 0.3171 time to fit residues: 103.4847 Evaluate side-chains 243 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1589 GLU Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 348 GLN A 986 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11292 Z= 0.250 Angle : 0.576 8.626 15391 Z= 0.297 Chirality : 0.045 0.238 1653 Planarity : 0.005 0.061 1868 Dihedral : 17.834 179.929 1929 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.17 % Allowed : 21.67 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1259 helix: 1.56 (0.29), residues: 325 sheet: 0.65 (0.36), residues: 185 loop : -1.33 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.005 0.001 HIS A1621 PHE 0.016 0.002 PHE A 546 TYR 0.015 0.001 TYR A 987 ARG 0.004 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 1.260 Fit side-chains REVERT: A 27 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6056 (m-30) REVERT: A 51 ARG cc_start: 0.8389 (ptp-170) cc_final: 0.8082 (mtp-110) REVERT: A 170 VAL cc_start: 0.7996 (m) cc_final: 0.7758 (t) REVERT: A 206 THR cc_start: 0.8580 (t) cc_final: 0.8166 (m) REVERT: A 287 ASN cc_start: 0.7897 (m110) cc_final: 0.7658 (m110) REVERT: A 651 PHE cc_start: 0.8415 (m-10) cc_final: 0.8080 (m-80) REVERT: A 653 GLU cc_start: 0.6857 (mp0) cc_final: 0.6518 (mp0) REVERT: A 739 THR cc_start: 0.8501 (m) cc_final: 0.8037 (p) REVERT: A 748 GLU cc_start: 0.7397 (pp20) cc_final: 0.6989 (pp20) REVERT: A 763 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: A 944 GLU cc_start: 0.7266 (pm20) cc_final: 0.6981 (pm20) REVERT: A 1389 LYS cc_start: 0.5337 (mmtm) cc_final: 0.5079 (ttpt) REVERT: A 1401 LYS cc_start: 0.8085 (tttt) cc_final: 0.7846 (tptt) REVERT: A 1589 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6675 (tm-30) outliers start: 35 outliers final: 26 residues processed: 244 average time/residue: 0.3255 time to fit residues: 104.8740 Evaluate side-chains 248 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1589 GLU Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 348 GLN A 433 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 11292 Z= 0.364 Angle : 0.632 9.488 15391 Z= 0.328 Chirality : 0.048 0.253 1653 Planarity : 0.005 0.061 1868 Dihedral : 17.930 179.438 1929 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.90 % Allowed : 22.03 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1259 helix: 1.27 (0.29), residues: 331 sheet: 0.55 (0.36), residues: 195 loop : -1.37 (0.20), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 612 HIS 0.008 0.002 HIS A 984 PHE 0.017 0.002 PHE A 192 TYR 0.016 0.002 TYR A 987 ARG 0.006 0.000 ARG A 738 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 1.246 Fit side-chains REVERT: A 27 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6243 (m-30) REVERT: A 51 ARG cc_start: 0.8422 (ptp-170) cc_final: 0.8086 (mtp-110) REVERT: A 206 THR cc_start: 0.8638 (t) cc_final: 0.8297 (m) REVERT: A 287 ASN cc_start: 0.8001 (m110) cc_final: 0.7772 (m110) REVERT: A 522 SER cc_start: 0.8404 (m) cc_final: 0.8056 (p) REVERT: A 651 PHE cc_start: 0.8447 (m-10) cc_final: 0.8171 (m-80) REVERT: A 748 GLU cc_start: 0.7338 (pp20) cc_final: 0.6919 (pp20) REVERT: A 763 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7068 (tt0) REVERT: A 944 GLU cc_start: 0.7310 (pm20) cc_final: 0.7021 (pm20) REVERT: A 977 LEU cc_start: 0.8066 (mt) cc_final: 0.7823 (mp) REVERT: A 1389 LYS cc_start: 0.5461 (mmtm) cc_final: 0.5148 (ttpp) outliers start: 32 outliers final: 28 residues processed: 246 average time/residue: 0.3370 time to fit residues: 111.7951 Evaluate side-chains 253 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.0370 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 119 optimal weight: 0.0970 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 348 GLN A 433 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11292 Z= 0.160 Angle : 0.541 7.265 15391 Z= 0.281 Chirality : 0.043 0.230 1653 Planarity : 0.005 0.061 1868 Dihedral : 17.760 179.692 1929 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.99 % Allowed : 22.85 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1259 helix: 1.71 (0.29), residues: 324 sheet: 0.62 (0.36), residues: 188 loop : -1.31 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 PHE 0.012 0.001 PHE A 824 TYR 0.009 0.001 TYR A 529 ARG 0.004 0.000 ARG A 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 1.231 Fit side-chains REVERT: A 27 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.5867 (m-30) REVERT: A 51 ARG cc_start: 0.8318 (ptp-170) cc_final: 0.8038 (mtp-110) REVERT: A 206 THR cc_start: 0.8447 (t) cc_final: 0.8088 (m) REVERT: A 229 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8203 (mtpt) REVERT: A 287 ASN cc_start: 0.7836 (m110) cc_final: 0.7592 (m110) REVERT: A 651 PHE cc_start: 0.8354 (m-10) cc_final: 0.8063 (m-80) REVERT: A 739 THR cc_start: 0.8460 (m) cc_final: 0.8071 (p) REVERT: A 748 GLU cc_start: 0.7323 (pp20) cc_final: 0.6992 (pp20) REVERT: A 763 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: A 800 LEU cc_start: 0.8025 (tp) cc_final: 0.7823 (mp) REVERT: A 944 GLU cc_start: 0.7271 (pm20) cc_final: 0.6982 (pm20) REVERT: A 977 LEU cc_start: 0.8130 (mt) cc_final: 0.7892 (mp) REVERT: A 1389 LYS cc_start: 0.5316 (mmtm) cc_final: 0.5089 (ttpp) REVERT: A 1570 PHE cc_start: 0.8264 (p90) cc_final: 0.7793 (p90) outliers start: 22 outliers final: 19 residues processed: 240 average time/residue: 0.3137 time to fit residues: 100.6938 Evaluate side-chains 242 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.0770 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 348 GLN A 433 GLN A 986 ASN A1596 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.094860 restraints weight = 15219.605| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.87 r_work: 0.3034 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11292 Z= 0.167 Angle : 0.536 8.169 15391 Z= 0.276 Chirality : 0.042 0.227 1653 Planarity : 0.004 0.062 1868 Dihedral : 17.706 178.979 1929 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.72 % Allowed : 22.76 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1259 helix: 1.79 (0.29), residues: 324 sheet: 0.45 (0.36), residues: 198 loop : -1.27 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 PHE 0.012 0.001 PHE A 824 TYR 0.010 0.001 TYR A 987 ARG 0.004 0.000 ARG A 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2980.88 seconds wall clock time: 55 minutes 22.90 seconds (3322.90 seconds total)