Starting phenix.real_space_refine on Sun Apr 7 00:16:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/04_2024/7rtm_24683_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/04_2024/7rtm_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_24683/04_2024/7rtm_24683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/04_2024/7rtm_24683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/04_2024/7rtm_24683_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/04_2024/7rtm_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-dev-5288/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: 5.43, per 1000 atoms: 0.59 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: 3.75 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: 1.97 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: 3.35 Time building geometry restraints manager: 4.02 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: 0.980 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: 0.010 Extract box with map and model: 3.750 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.340 Find NCS groups from input model: 0.530 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: 0.550 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.360 ------------------------------------------------------------------------------- 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 : 1.037 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 REVERT: A 988 VAL cc_start: 0.2821 (p) cc_final: 0.2144 (t) REVERT: B 700 ILE cc_start: 0.4583 (mt) cc_final: 0.4293 (mt) REVERT: B 881 THR cc_start: 0.4669 (p) cc_final: 0.4140 (p) REVERT: B 988 VAL cc_start: 0.3922 (p) cc_final: 0.3317 (t) outliers start: 28 outliers final: 5 residues processed: 373 average time/residue: 0.2096 time to fit residues: 107.4121 Evaluate side-chains 202 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 691 THR 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 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 822 HIS B 855 ASN B 869 GLN B 923 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5257 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9411 Z= 0.270 Angle : 0.878 12.133 12795 Z= 0.441 Chirality : 0.049 0.243 1504 Planarity : 0.007 0.067 1548 Dihedral : 13.349 112.773 1390 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.05 % Rotamer: Outliers : 3.50 % Allowed : 17.28 % Favored : 79.22 % 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: -0.57 (0.24), residues: 1138 helix: 0.26 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 467 HIS 0.014 0.002 HIS A 937 PHE 0.022 0.003 PHE A 496 TYR 0.033 0.002 TYR B 486 ARG 0.006 0.001 ARG B 876 *********************** 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 230 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 195 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 906 VAL cc_start: 0.4829 (p) cc_final: 0.3668 (t) outliers start: 35 outliers final: 20 residues processed: 221 average time/residue: 0.1922 time to fit residues: 60.8521 Evaluate side-chains 168 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5471 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9411 Z= 0.236 Angle : 0.767 10.469 12795 Z= 0.380 Chirality : 0.046 0.223 1504 Planarity : 0.005 0.055 1548 Dihedral : 12.012 105.743 1384 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 4.30 % Allowed : 17.18 % Favored : 78.52 % 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 (0.24), residues: 1138 helix: 0.52 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -1.09 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 465 HIS 0.016 0.002 HIS B 647 PHE 0.018 0.002 PHE A 925 TYR 0.052 0.002 TYR A 486 ARG 0.007 0.001 ARG B 471 *********************** 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 213 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 170 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 831 MET cc_start: 0.4194 (mmm) cc_final: 0.3794 (mmm) REVERT: A 879 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.4486 (ttm170) REVERT: B 490 MET cc_start: 0.5533 (OUTLIER) cc_final: 0.4970 (ttt) REVERT: B 906 VAL cc_start: 0.5733 (p) cc_final: 0.4654 (t) outliers start: 43 outliers final: 24 residues processed: 206 average time/residue: 0.1677 time to fit residues: 51.5994 Evaluate side-chains 160 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 879 ARG Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 855 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9411 Z= 0.283 Angle : 0.781 11.315 12795 Z= 0.383 Chirality : 0.046 0.196 1504 Planarity : 0.005 0.054 1548 Dihedral : 10.997 94.796 1383 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 5.39 % Allowed : 18.38 % Favored : 76.22 % 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: -0.20 (0.25), residues: 1138 helix: 0.46 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.98 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 465 HIS 0.010 0.001 HIS B 647 PHE 0.022 0.002 PHE A 484 TYR 0.019 0.002 TYR A 486 ARG 0.006 0.001 ARG B 950 *********************** 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 220 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 166 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 PHE cc_start: 0.5719 (t80) cc_final: 0.5321 (t80) REVERT: B 739 PHE cc_start: 0.5029 (OUTLIER) cc_final: 0.4656 (m-80) REVERT: B 831 MET cc_start: 0.4771 (mmm) cc_final: 0.4117 (mmm) outliers start: 54 outliers final: 33 residues processed: 207 average time/residue: 0.1623 time to fit residues: 50.6416 Evaluate side-chains 161 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- 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 822 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.7536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9411 Z= 0.210 Angle : 0.700 10.763 12795 Z= 0.337 Chirality : 0.044 0.235 1504 Planarity : 0.004 0.054 1548 Dihedral : 10.281 89.236 1383 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 3.50 % Allowed : 21.68 % Favored : 74.83 % 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: -0.09 (0.25), residues: 1138 helix: 0.63 (0.20), residues: 693 sheet: None (None), residues: 0 loop : -1.10 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 569 HIS 0.007 0.001 HIS A 630 PHE 0.020 0.002 PHE B 987 TYR 0.013 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 179 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 741 MET cc_start: 0.6642 (mmt) cc_final: 0.6152 (mmt) REVERT: A 895 MET cc_start: 0.3573 (tmm) cc_final: 0.3069 (tmm) REVERT: B 739 PHE cc_start: 0.5423 (OUTLIER) cc_final: 0.4922 (m-80) outliers start: 35 outliers final: 21 residues processed: 172 average time/residue: 0.1782 time to fit residues: 45.5502 Evaluate side-chains 143 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 930 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN B 822 HIS B 953 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.8509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9411 Z= 0.276 Angle : 0.738 9.571 12795 Z= 0.359 Chirality : 0.046 0.240 1504 Planarity : 0.005 0.053 1548 Dihedral : 9.744 82.280 1382 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 4.50 % Allowed : 21.38 % Favored : 74.13 % 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: 0.56 (0.19), residues: 705 sheet: None (None), residues: 0 loop : -1.24 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 465 HIS 0.007 0.001 HIS A 630 PHE 0.024 0.002 PHE A 484 TYR 0.019 0.002 TYR B 486 ARG 0.005 0.001 ARG B 950 *********************** 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 181 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 136 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8246 (mt) REVERT: A 741 MET cc_start: 0.6804 (mmt) cc_final: 0.6466 (mmt) REVERT: B 739 PHE cc_start: 0.5473 (OUTLIER) cc_final: 0.4773 (m-80) outliers start: 45 outliers final: 28 residues processed: 173 average time/residue: 0.1542 time to fit residues: 40.8646 Evaluate side-chains 150 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 799 MET Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 902 ILE Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 ASN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.8872 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= 0.208 Angle : 0.735 13.850 12795 Z= 0.343 Chirality : 0.044 0.257 1504 Planarity : 0.004 0.054 1548 Dihedral : 9.227 77.228 1382 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.71 % Favored : 94.20 % Rotamer: Outliers : 4.10 % Allowed : 22.98 % Favored : 72.93 % 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: -0.10 (0.25), residues: 1138 helix: 0.66 (0.19), residues: 707 sheet: None (None), residues: 0 loop : -1.24 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 569 HIS 0.005 0.001 HIS A 630 PHE 0.015 0.002 PHE A 515 TYR 0.014 0.001 TYR B 486 ARG 0.005 0.000 ARG A 765 *********************** 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 174 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8246 (mt) REVERT: A 741 MET cc_start: 0.6775 (mmt) cc_final: 0.6483 (mmt) REVERT: A 895 MET cc_start: 0.4670 (tmm) cc_final: 0.4378 (tmm) REVERT: B 739 PHE cc_start: 0.5236 (OUTLIER) cc_final: 0.4546 (m-80) REVERT: B 857 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4812 (pp) outliers start: 41 outliers final: 27 residues processed: 168 average time/residue: 0.1565 time to fit residues: 40.7153 Evaluate side-chains 151 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 686 HIS Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 902 ILE Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 105 optimal weight: 0.0020 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 959 GLN B 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.9066 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= 0.184 Angle : 0.725 13.290 12795 Z= 0.339 Chirality : 0.043 0.263 1504 Planarity : 0.004 0.053 1548 Dihedral : 8.642 74.003 1382 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 3.40 % Allowed : 23.98 % Favored : 72.63 % 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: 0.17 (0.25), residues: 1138 helix: 0.86 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -0.99 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 967 HIS 0.004 0.001 HIS A 630 PHE 0.020 0.001 PHE B 544 TYR 0.010 0.001 TYR B 486 ARG 0.002 0.000 ARG B 768 *********************** 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 170 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8278 (mt) REVERT: A 741 MET cc_start: 0.6788 (mmt) cc_final: 0.6475 (mmt) REVERT: A 825 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6919 (tt) REVERT: A 895 MET cc_start: 0.4877 (tmm) cc_final: 0.4629 (tmm) REVERT: B 739 PHE cc_start: 0.5237 (OUTLIER) cc_final: 0.4514 (m-80) outliers start: 34 outliers final: 21 residues processed: 162 average time/residue: 0.1712 time to fit residues: 41.6420 Evaluate side-chains 150 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 105 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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: 0.6244 moved from start: 0.9246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9411 Z= 0.178 Angle : 0.737 12.545 12795 Z= 0.343 Chirality : 0.043 0.276 1504 Planarity : 0.004 0.054 1548 Dihedral : 8.226 73.138 1382 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.36 % Favored : 94.55 % Rotamer: Outliers : 2.80 % Allowed : 24.88 % Favored : 72.33 % 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: 0.18 (0.25), residues: 1138 helix: 0.85 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.95 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 697 HIS 0.007 0.001 HIS A 686 PHE 0.028 0.001 PHE B 544 TYR 0.010 0.001 TYR B 486 ARG 0.002 0.000 ARG B 876 *********************** 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 157 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8195 (mt) REVERT: A 741 MET cc_start: 0.6729 (mmt) cc_final: 0.6363 (mmt) REVERT: A 825 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6919 (tt) REVERT: A 831 MET cc_start: 0.5079 (mmm) cc_final: 0.4366 (mmm) REVERT: A 895 MET cc_start: 0.4923 (tmm) cc_final: 0.4708 (tmm) REVERT: B 739 PHE cc_start: 0.5062 (OUTLIER) cc_final: 0.4429 (m-80) REVERT: B 831 MET cc_start: 0.5628 (mmm) cc_final: 0.5016 (mmm) outliers start: 28 outliers final: 23 residues processed: 150 average time/residue: 0.1641 time to fit residues: 37.4654 Evaluate side-chains 149 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.9542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9411 Z= 0.229 Angle : 0.747 14.146 12795 Z= 0.353 Chirality : 0.044 0.248 1504 Planarity : 0.005 0.053 1548 Dihedral : 7.846 71.862 1382 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.71 % Favored : 94.20 % Rotamer: Outliers : 2.60 % Allowed : 24.98 % Favored : 72.43 % 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: 0.20 (0.25), residues: 1138 helix: 0.87 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.95 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 697 HIS 0.004 0.001 HIS A 630 PHE 0.029 0.002 PHE A 515 TYR 0.014 0.001 TYR B 486 ARG 0.003 0.000 ARG B 989 ********************** 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 148 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 701 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8262 (mt) REVERT: A 741 MET cc_start: 0.6951 (mmt) cc_final: 0.6650 (mmt) REVERT: A 825 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.7008 (tt) REVERT: A 831 MET cc_start: 0.5264 (mmm) cc_final: 0.4497 (mmm) REVERT: B 831 MET cc_start: 0.5975 (mmm) cc_final: 0.5510 (mmm) outliers start: 26 outliers final: 22 residues processed: 142 average time/residue: 0.1587 time to fit residues: 34.3551 Evaluate side-chains 139 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 65 optimal weight: 0.0060 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.115654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.096833 restraints weight = 28200.270| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.50 r_work: 0.3548 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.9652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9411 Z= 0.175 Angle : 0.753 13.153 12795 Z= 0.350 Chirality : 0.044 0.244 1504 Planarity : 0.004 0.055 1548 Dihedral : 7.443 71.309 1382 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 2.20 % Allowed : 26.17 % Favored : 71.63 % 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: 0.92 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.91 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 697 HIS 0.004 0.001 HIS A 813 PHE 0.037 0.002 PHE B 544 TYR 0.010 0.001 TYR B 486 ARG 0.002 0.000 ARG B 768 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2149.84 seconds wall clock time: 39 minutes 58.41 seconds (2398.41 seconds total)