Starting phenix.real_space_refine on Fri Dec 8 21:20:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/12_2023/7rtm_24683_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/12_2023/7rtm_24683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/12_2023/7rtm_24683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/12_2023/7rtm_24683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/12_2023/7rtm_24683_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/12_2023/7rtm_24683_updated.pdb" } resolution = 3.4 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 76 5.16 5 Na 2 4.78 5 C 6052 2.51 5 N 1452 2.21 5 O 1579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 471": "NH1" <-> "NH2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A ARG 726": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ARG 810": "NH1" <-> "NH2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 876": "NH1" <-> "NH2" Residue "A GLU 877": "OE1" <-> "OE2" Residue "A PHE 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 945": "NH1" <-> "NH2" Residue "B ARG 471": "NH1" <-> "NH2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B GLU 545": "OE1" <-> "OE2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B GLU 642": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B ARG 726": "NH1" <-> "NH2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 768": "NH1" <-> "NH2" Residue "B ARG 810": "NH1" <-> "NH2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "B ARG 876": "NH1" <-> "NH2" Residue "B GLU 877": "OE1" <-> "OE2" Residue "B ARG 945": "NH1" <-> "NH2" Residue "B PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9161 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4520 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 30, 'TRANS': 540} Chain: "B" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4519 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 540} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {' NA': 1, 'CO3': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {' NA': 1, 'CO3': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1051 residue: pdb=" N LEU A 451 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 451 " occ=0.00 residue: pdb=" N PHE A 452 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 452 " occ=0.00 residue: pdb=" N GLY A 453 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 453 " occ=0.00 residue: pdb=" N GLY A 454 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 454 " occ=0.00 residue: pdb=" N LEU A 455 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 455 " occ=0.00 residue: pdb=" N VAL A 456 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL A 456 " occ=0.00 residue: pdb=" N LEU A 457 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 457 " occ=0.00 residue: pdb=" N ASP A 458 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 458 " occ=0.00 residue: pdb=" N VAL A 459 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL A 459 " occ=0.00 residue: pdb=" N LYS A 460 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 460 " occ=0.00 residue: pdb=" N ARG A 461 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 461 " occ=0.00 residue: pdb=" N LYS A 462 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 462 " occ=0.00 ... (remaining 1039 not shown) Time building chain proxies: 5.13, per 1000 atoms: 0.56 Number of scatterers: 9161 At special positions: 0 Unit cell: (130.54, 85.6, 108.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 Na 2 11.00 O 1579 8.00 N 1452 7.00 C 6052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 636 " - pdb=" SG CYS A 684 " distance=1.98 Simple disulfide: pdb=" SG CYS A 638 " - pdb=" SG CYS A 672 " distance=2.07 Simple disulfide: pdb=" SG CYS B 636 " - pdb=" SG CYS B 684 " distance=1.73 Simple disulfide: pdb=" SG CYS B 638 " - pdb=" SG CYS B 672 " distance=2.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " NAG C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 2 sheets defined 61.4% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 479 through 492 removed outlier: 3.814A pdb=" N CYS A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 491 " --> pdb=" O CYS A 487 " (cutoff:3.500A) Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 495 through 503 removed outlier: 3.791A pdb=" N ALA A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 527 removed outlier: 3.570A pdb=" N LEU A 526 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 removed outlier: 3.786A pdb=" N LYS A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 580 removed outlier: 3.612A pdb=" N THR A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'A' and resid 591 through 619 removed outlier: 3.637A pdb=" N LEU A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 4.355A pdb=" N SER A 632 " --> pdb=" O ASP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 654 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.570A pdb=" N GLU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 717 removed outlier: 3.910A pdb=" N SER A 710 " --> pdb=" O PHE A 706 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N THR A 717 " --> pdb=" O LYS A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 747 removed outlier: 4.137A pdb=" N THR A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 729 " --> pdb=" O VAL A 725 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 730 " --> pdb=" O ARG A 726 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 732 " --> pdb=" O THR A 728 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE A 735 " --> pdb=" O ASP A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 808 removed outlier: 3.824A pdb=" N ILE A 784 " --> pdb=" O TRP A 780 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 787 " --> pdb=" O VAL A 783 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE A 788 " --> pdb=" O ILE A 784 " (cutoff:3.500A) Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 821 through 837 Processing helix chain 'A' and resid 847 through 856 Processing helix chain 'A' and resid 881 through 891 Processing helix chain 'A' and resid 904 through 920 removed outlier: 4.267A pdb=" N LEU A 919 " --> pdb=" O GLY A 915 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN A 920 " --> pdb=" O VAL A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 930 Processing helix chain 'A' and resid 942 through 946 removed outlier: 4.026A pdb=" N ARG A 945 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A 946 " --> pdb=" O TYR A 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 946' Processing helix chain 'A' and resid 949 through 970 Processing helix chain 'A' and resid 976 through 978 No H-bonds generated for 'chain 'A' and resid 976 through 978' Processing helix chain 'A' and resid 980 through 995 removed outlier: 4.400A pdb=" N VAL A 988 " --> pdb=" O LEU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1001 No H-bonds generated for 'chain 'A' and resid 999 through 1001' Processing helix chain 'A' and resid 1010 through 1020 Processing helix chain 'B' and resid 456 through 469 Proline residue: B 464 - end of helix removed outlier: 4.610A pdb=" N TRP B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER B 468 " --> pdb=" O PRO B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 503 removed outlier: 3.603A pdb=" N SER B 491 " --> pdb=" O CYS B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix removed outlier: 4.072A pdb=" N ALA B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 527 removed outlier: 3.840A pdb=" N LEU B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 553 removed outlier: 3.515A pdb=" N LYS B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 580 Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 591 through 619 Processing helix chain 'B' and resid 628 through 633 removed outlier: 4.359A pdb=" N SER B 632 " --> pdb=" O ASP B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 654 Processing helix chain 'B' and resid 661 through 663 No H-bonds generated for 'chain 'B' and resid 661 through 663' Processing helix chain 'B' and resid 669 through 674 removed outlier: 3.922A pdb=" N GLN B 673 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 669 through 674' Processing helix chain 'B' and resid 694 through 713 removed outlier: 3.661A pdb=" N ILE B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 710 " --> pdb=" O PHE B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'B' and resid 723 through 726 No H-bonds generated for 'chain 'B' and resid 723 through 726' Processing helix chain 'B' and resid 733 through 747 Processing helix chain 'B' and resid 764 through 766 No H-bonds generated for 'chain 'B' and resid 764 through 766' Processing helix chain 'B' and resid 780 through 808 removed outlier: 3.894A pdb=" N ILE B 784 " --> pdb=" O TRP B 780 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE B 787 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE B 788 " --> pdb=" O ILE B 784 " (cutoff:3.500A) Proline residue: B 789 - end of helix removed outlier: 3.515A pdb=" N ILE B 795 " --> pdb=" O LEU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 837 Processing helix chain 'B' and resid 847 through 856 Processing helix chain 'B' and resid 881 through 893 removed outlier: 4.475A pdb=" N VAL B 893 " --> pdb=" O MET B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 900 No H-bonds generated for 'chain 'B' and resid 897 through 900' Processing helix chain 'B' and resid 904 through 920 removed outlier: 4.013A pdb=" N LEU B 919 " --> pdb=" O GLY B 915 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN B 920 " --> pdb=" O VAL B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 930 removed outlier: 3.576A pdb=" N ARG B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 930 " --> pdb=" O ASP B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 949 through 971 Processing helix chain 'B' and resid 976 through 995 Proline residue: B 979 - end of helix removed outlier: 4.480A pdb=" N VAL B 988 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 990 " --> pdb=" O PHE B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1000 No H-bonds generated for 'chain 'B' and resid 998 through 1000' Processing helix chain 'B' and resid 1010 through 1018 Processing sheet with id= A, first strand: chain 'A' and resid 636 through 639 Processing sheet with id= B, first strand: chain 'B' and resid 636 through 639 438 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 1448 1.32 - 1.47: 3650 1.47 - 1.63: 4191 1.63 - 1.78: 21 1.78 - 1.94: 101 Bond restraints: 9411 Sorted by residual: bond pdb=" CA GLY B 501 " pdb=" C GLY B 501 " ideal model delta sigma weight residual 1.516 1.387 0.129 1.09e-02 8.42e+03 1.41e+02 bond pdb=" NE ARG A 471 " pdb=" CZ ARG A 471 " ideal model delta sigma weight residual 1.326 1.444 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" C ALA A 897 " pdb=" N VAL A 898 " ideal model delta sigma weight residual 1.335 1.463 -0.129 1.26e-02 6.30e+03 1.04e+02 bond pdb=" N PHE B 702 " pdb=" CA PHE B 702 " ideal model delta sigma weight residual 1.459 1.345 0.114 1.17e-02 7.31e+03 9.44e+01 bond pdb=" ND1 HIS B 625 " pdb=" CE1 HIS B 625 " ideal model delta sigma weight residual 1.321 1.416 -0.095 1.00e-02 1.00e+04 9.11e+01 ... (remaining 9406 not shown) Histogram of bond angle deviations from ideal: 88.65 - 98.68: 31 98.68 - 108.71: 1404 108.71 - 118.75: 6579 118.75 - 128.78: 4624 128.78 - 138.81: 157 Bond angle restraints: 12795 Sorted by residual: angle pdb=" N VAL A 893 " pdb=" CA VAL A 893 " pdb=" C VAL A 893 " ideal model delta sigma weight residual 113.53 102.71 10.82 9.80e-01 1.04e+00 1.22e+02 angle pdb=" CA ALA B 463 " pdb=" C ALA B 463 " pdb=" N PRO B 464 " ideal model delta sigma weight residual 120.93 132.26 -11.33 1.06e+00 8.90e-01 1.14e+02 angle pdb=" CA ALA B 463 " pdb=" C ALA B 463 " pdb=" O ALA B 463 " ideal model delta sigma weight residual 118.34 108.90 9.44 9.70e-01 1.06e+00 9.47e+01 angle pdb=" N GLN B 920 " pdb=" CA GLN B 920 " pdb=" C GLN B 920 " ideal model delta sigma weight residual 113.23 101.30 11.93 1.24e+00 6.50e-01 9.26e+01 angle pdb=" N GLU B1010 " pdb=" CA GLU B1010 " pdb=" C GLU B1010 " ideal model delta sigma weight residual 111.71 122.71 -11.00 1.15e+00 7.56e-01 9.15e+01 ... (remaining 12790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.66: 5358 24.66 - 49.31: 213 49.31 - 73.97: 45 73.97 - 98.62: 21 98.62 - 123.28: 10 Dihedral angle restraints: 5647 sinusoidal: 2311 harmonic: 3336 Sorted by residual: dihedral pdb=" C SER A 468 " pdb=" N SER A 468 " pdb=" CA SER A 468 " pdb=" CB SER A 468 " ideal model delta harmonic sigma weight residual -122.60 -140.76 18.16 0 2.50e+00 1.60e-01 5.28e+01 dihedral pdb=" N MET B 981 " pdb=" C MET B 981 " pdb=" CA MET B 981 " pdb=" CB MET B 981 " ideal model delta harmonic sigma weight residual 122.80 139.52 -16.72 0 2.50e+00 1.60e-01 4.47e+01 dihedral pdb=" C GLU B1010 " pdb=" N GLU B1010 " pdb=" CA GLU B1010 " pdb=" CB GLU B1010 " ideal model delta harmonic sigma weight residual -122.60 -138.66 16.06 0 2.50e+00 1.60e-01 4.13e+01 ... (remaining 5644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 944 0.147 - 0.294: 389 0.294 - 0.442: 130 0.442 - 0.589: 35 0.589 - 0.736: 6 Chirality restraints: 1504 Sorted by residual: chirality pdb=" C1 NAG D 3 " pdb=" O4 NAG D 2 " pdb=" C2 NAG D 3 " pdb=" O5 NAG D 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.78e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.61e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.18e+01 ... (remaining 1501 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 3 " 0.313 2.00e-02 2.50e+03 2.69e-01 9.04e+02 pdb=" C7 NAG D 3 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG D 3 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG D 3 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG D 3 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.305 2.00e-02 2.50e+03 2.63e-01 8.61e+02 pdb=" C7 NAG D 2 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.002 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.449 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.270 2.00e-02 2.50e+03 2.30e-01 6.64e+02 pdb=" C7 NAG D 1 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.398 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.026 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 8 1.82 - 2.59: 172 2.59 - 3.36: 11788 3.36 - 4.13: 21410 4.13 - 4.90: 37456 Nonbonded interactions: 70834 Sorted by model distance: nonbonded pdb=" CD2 HIS A 937 " pdb=" CB PRO B 866 " model vdw 1.051 3.660 nonbonded pdb=" O ALA A 845 " pdb="NA NA A1102 " model vdw 1.122 2.470 nonbonded pdb=" O LEU A 476 " pdb=" OD2 ASP A 731 " model vdw 1.520 3.040 nonbonded pdb=" SG CYS A 565 " pdb=" CD1 ILE A 775 " model vdw 1.625 3.820 nonbonded pdb=" CD1 PHE A 484 " pdb=" CG1 VAL A 734 " model vdw 1.667 3.760 ... (remaining 70829 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 451 through 772 or (resid 773 and (name N or name CA or na \ me C or name O or name CB )) or resid 774 through 1021 or resid 1101 through 110 \ 3)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.06 Reset to 1. 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 3.740 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.110 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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: 0.580 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4590 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 : 0.031 0.131 9411 Z= 2.001 Angle : 3.049 13.876 12795 Z= 2.132 Chirality : 0.185 0.736 1504 Planarity : 0.028 0.269 1548 Dihedral : 16.560 123.278 3475 Min Nonbonded Distance : 1.051 Molprobity Statistics. All-atom Clashscore : 36.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.77 % Favored : 92.97 % Rotamer: Outliers : 2.80 % Allowed : 9.29 % Favored : 87.91 % Cbeta Deviations : 4.07 % 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: -1.12 (0.23), residues: 1138 helix: 0.06 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -1.93 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.275 0.042 TRP B 467 HIS 0.043 0.007 HIS B 822 PHE 0.214 0.030 PHE B 955 TYR 0.184 0.042 TYR A 607 ARG 0.055 0.007 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 352 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 5 residues processed: 373 average time/residue: 0.2064 time to fit residues: 105.7724 Evaluate side-chains 203 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 198 time to evaluate : 1.011 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0893 time to fit residues: 2.1152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS A 647 HIS A 655 HIS A 663 ASN A 686 HIS A 923 GLN A 937 HIS ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN B 643 ASN B 646 ASN B 676 HIS B 686 HIS B 855 ASN B 869 GLN B 923 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5263 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9411 Z= 0.260 Angle : 0.867 13.133 12795 Z= 0.435 Chirality : 0.049 0.246 1504 Planarity : 0.007 0.067 1548 Dihedral : 13.070 112.214 1382 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 3.60 % Allowed : 16.68 % Favored : 79.72 % 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: -0.52 (0.24), residues: 1138 helix: 0.30 (0.19), residues: 693 sheet: None (None), residues: 0 loop : -1.29 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 467 HIS 0.012 0.002 HIS A 630 PHE 0.024 0.003 PHE A 496 TYR 0.034 0.003 TYR B 486 ARG 0.005 0.001 ARG A 927 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 193 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 218 average time/residue: 0.1868 time to fit residues: 58.6914 Evaluate side-chains 173 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0848 time to fit residues: 4.4962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.0070 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5390 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9411 Z= 0.215 Angle : 0.761 10.263 12795 Z= 0.376 Chirality : 0.046 0.241 1504 Planarity : 0.005 0.056 1548 Dihedral : 12.113 106.560 1382 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 2.60 % Allowed : 17.18 % Favored : 80.22 % 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 (0.24), residues: 1138 helix: 0.50 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.08 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 465 HIS 0.017 0.002 HIS B 647 PHE 0.022 0.002 PHE B 679 TYR 0.048 0.002 TYR A 486 ARG 0.005 0.001 ARG A 591 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 7 residues processed: 189 average time/residue: 0.1694 time to fit residues: 47.9003 Evaluate side-chains 142 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0920 time to fit residues: 2.5902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 0.0030 chunk 29 optimal weight: 4.9990 overall best weight: 0.5952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5539 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9411 Z= 0.194 Angle : 0.721 10.378 12795 Z= 0.348 Chirality : 0.044 0.199 1504 Planarity : 0.005 0.057 1548 Dihedral : 11.276 99.045 1382 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 2.60 % Allowed : 18.68 % Favored : 78.72 % 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: 0.04 (0.24), residues: 1138 helix: 0.72 (0.20), residues: 675 sheet: None (None), residues: 0 loop : -0.95 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 465 HIS 0.014 0.001 HIS B 647 PHE 0.018 0.002 PHE A 544 TYR 0.051 0.002 TYR A 486 ARG 0.004 0.000 ARG B 507 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.247 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 175 average time/residue: 0.1671 time to fit residues: 44.1485 Evaluate side-chains 144 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0871 time to fit residues: 2.8705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 855 ASN B 855 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9411 Z= 0.217 Angle : 0.695 10.424 12795 Z= 0.340 Chirality : 0.045 0.231 1504 Planarity : 0.005 0.055 1548 Dihedral : 10.309 88.597 1382 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 2.70 % Allowed : 19.68 % Favored : 77.62 % 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: 0.19 (0.25), residues: 1138 helix: 0.82 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.87 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 465 HIS 0.008 0.001 HIS A 630 PHE 0.018 0.002 PHE B 515 TYR 0.025 0.001 TYR A 486 ARG 0.002 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.172 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 169 average time/residue: 0.1838 time to fit residues: 46.5252 Evaluate side-chains 148 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0973 time to fit residues: 4.5797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 0.0670 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.7422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9411 Z= 0.218 Angle : 0.711 12.994 12795 Z= 0.341 Chirality : 0.043 0.246 1504 Planarity : 0.005 0.054 1548 Dihedral : 9.845 84.277 1382 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 2.20 % Allowed : 21.18 % Favored : 76.62 % 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: 0.22 (0.25), residues: 1138 helix: 0.83 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.85 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 465 HIS 0.006 0.001 HIS A 630 PHE 0.024 0.002 PHE B 987 TYR 0.045 0.002 TYR A 486 ARG 0.002 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.059 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 155 average time/residue: 0.1596 time to fit residues: 38.0308 Evaluate side-chains 144 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1282 time to fit residues: 3.9576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.0870 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 855 ASN A 920 GLN B 646 ASN B 801 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.7861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9411 Z= 0.190 Angle : 0.713 11.999 12795 Z= 0.336 Chirality : 0.044 0.262 1504 Planarity : 0.004 0.054 1548 Dihedral : 9.196 76.544 1382 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 1.40 % Allowed : 21.98 % Favored : 76.62 % 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: 0.14 (0.25), residues: 1138 helix: 0.81 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.00 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 664 HIS 0.005 0.001 HIS A 630 PHE 0.025 0.002 PHE B 987 TYR 0.011 0.001 TYR A 486 ARG 0.002 0.000 ARG B 768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 159 average time/residue: 0.1905 time to fit residues: 45.5479 Evaluate side-chains 130 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1003 time to fit residues: 1.9216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0870 chunk 65 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 801 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.8160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9411 Z= 0.188 Angle : 0.744 10.999 12795 Z= 0.345 Chirality : 0.044 0.265 1504 Planarity : 0.004 0.055 1548 Dihedral : 8.823 74.335 1382 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 0.80 % Allowed : 23.68 % Favored : 75.52 % 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: 0.25 (0.25), residues: 1138 helix: 0.90 (0.20), residues: 691 sheet: None (None), residues: 0 loop : -0.93 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 465 HIS 0.005 0.001 HIS A 630 PHE 0.026 0.002 PHE B 987 TYR 0.012 0.001 TYR A 486 ARG 0.005 0.000 ARG B 989 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 144 average time/residue: 0.1826 time to fit residues: 39.2943 Evaluate side-chains 129 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0902 time to fit residues: 1.9583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.0020 chunk 80 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.8433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9411 Z= 0.176 Angle : 0.717 10.423 12795 Z= 0.335 Chirality : 0.043 0.264 1504 Planarity : 0.004 0.054 1548 Dihedral : 8.254 72.850 1382 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 0.70 % Allowed : 23.88 % Favored : 75.42 % 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: 0.31 (0.25), residues: 1138 helix: 0.95 (0.20), residues: 693 sheet: None (None), residues: 0 loop : -0.92 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 465 HIS 0.008 0.001 HIS B 625 PHE 0.042 0.001 PHE B 496 TYR 0.012 0.001 TYR A 486 ARG 0.003 0.000 ARG B 950 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 138 average time/residue: 0.1653 time to fit residues: 35.0951 Evaluate side-chains 128 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0866 time to fit residues: 1.6691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.0070 chunk 104 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 GLN B 855 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.8705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9411 Z= 0.195 Angle : 0.731 10.912 12795 Z= 0.343 Chirality : 0.044 0.255 1504 Planarity : 0.005 0.054 1548 Dihedral : 7.814 71.441 1382 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 0.30 % Allowed : 24.58 % Favored : 75.12 % 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 (0.25), residues: 1138 helix: 0.99 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.94 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 465 HIS 0.005 0.001 HIS B 625 PHE 0.034 0.002 PHE B 496 TYR 0.012 0.001 TYR B 690 ARG 0.002 0.000 ARG A 876 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.061 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.1616 time to fit residues: 32.4932 Evaluate side-chains 124 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0796 time to fit residues: 1.3870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.0050 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.117455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.098441 restraints weight = 28295.116| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.54 r_work: 0.3582 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.9206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 9411 Z= 0.223 Angle : 0.761 16.322 12795 Z= 0.356 Chirality : 0.045 0.220 1504 Planarity : 0.005 0.054 1548 Dihedral : 7.233 69.213 1382 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 0.30 % Allowed : 25.77 % Favored : 73.93 % 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: 0.27 (0.25), residues: 1138 helix: 0.93 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -0.90 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 465 HIS 0.004 0.001 HIS A 630 PHE 0.032 0.002 PHE B 496 TYR 0.014 0.001 TYR A 486 ARG 0.004 0.000 ARG B 950 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2009.96 seconds wall clock time: 37 minutes 20.50 seconds (2240.50 seconds total)