Starting phenix.real_space_refine (version: dev) on Tue Dec 13 10:54:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a70_6991/12_2022/6a70_6991.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a70_6991/12_2022/6a70_6991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a70_6991/12_2022/6a70_6991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a70_6991/12_2022/6a70_6991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a70_6991/12_2022/6a70_6991.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a70_6991/12_2022/6a70_6991.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 592": "NH1" <-> "NH2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3269": "NH1" <-> "NH2" Residue "B ARG 3662": "NH1" <-> "NH2" Residue "B ARG 3666": "NH1" <-> "NH2" Residue "B ARG 3672": "NH1" <-> "NH2" Residue "B ARG 3700": "NH1" <-> "NH2" Residue "B PHE 3714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3748": "NH1" <-> "NH2" Residue "B ARG 3750": "NH1" <-> "NH2" Residue "B ARG 3833": "NH1" <-> "NH2" Residue "B ARG 3848": "NH1" <-> "NH2" Residue "B ARG 3856": "NH1" <-> "NH2" Residue "B ARG 3870": "NH1" <-> "NH2" Residue "B ARG 3886": "NH1" <-> "NH2" Residue "B ARG 3891": "NH1" <-> "NH2" Residue "B ARG 3924": "NH1" <-> "NH2" Residue "B ARG 3927": "NH1" <-> "NH2" Residue "B ARG 3932": "NH1" <-> "NH2" Residue "B ARG 3965": "NH1" <-> "NH2" Residue "B ARG 3972": "NH1" <-> "NH2" Residue "B PHE 3974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3988": "NH1" <-> "NH2" Residue "B ARG 4021": "NH1" <-> "NH2" Residue "B ARG 4109": "NH1" <-> "NH2" Residue "F ARG 322": "NH1" <-> "NH2" Residue "F ARG 325": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 399": "NH1" <-> "NH2" Residue "F ARG 592": "NH1" <-> "NH2" Residue "F PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 251": "NH1" <-> "NH2" Residue "G ARG 322": "NH1" <-> "NH2" Residue "G ARG 325": "NH1" <-> "NH2" Residue "G ARG 355": "NH1" <-> "NH2" Residue "G PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 592": "NH1" <-> "NH2" Residue "G PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 15142 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 2579 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 306} Link IDs: {'PTRANS': 10, 'TRANS': 437} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1172 Unresolved non-hydrogen angles: 1526 Unresolved non-hydrogen dihedrals: 997 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 17, 'ASN:plan1': 19, 'TRP:plan': 8, 'ASP:plan': 16, 'PHE:plan': 28, 'GLU:plan': 18, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 681 Chain: "B" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 4960 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 24, 'TRANS': 679} Chain breaks: 6 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 627 Unresolved non-hydrogen angles: 817 Unresolved non-hydrogen dihedrals: 536 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 6, 'HIS:plan': 10, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 364 Chain: "F" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3762 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 452} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 3841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3841 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 460} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 9.26, per 1000 atoms: 0.61 Number of scatterers: 15142 At special positions: 0 Unit cell: (138.557, 120.01, 126.556, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 2695 8.00 N 2574 7.00 C 9812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=0, symmetry=0 Time building additional restraints: 5.94 Conformation dependent library (CDL) restraints added in 2.6 seconds 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 51.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 224 through 229 removed outlier: 4.526A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.633A pdb=" N LEU A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A 239 " --> pdb=" O CYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 removed outlier: 3.728A pdb=" N VAL A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.526A pdb=" N ARG A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 removed outlier: 3.881A pdb=" N GLU A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.570A pdb=" N ASP A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.558A pdb=" N THR A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 486 removed outlier: 3.732A pdb=" N PHE A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.898A pdb=" N VAL A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 563 through 577 removed outlier: 4.175A pdb=" N PHE A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 571 " --> pdb=" O PHE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 620 removed outlier: 4.174A pdb=" N LEU A 586 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 599 " --> pdb=" O LYS A 595 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 removed outlier: 3.878A pdb=" N PHE A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 638 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 639 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.553A pdb=" N ILE A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 692 removed outlier: 3.961A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 680 " --> pdb=" O PHE A 676 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 3076 through 3087 removed outlier: 3.699A pdb=" N THR B3080 " --> pdb=" O ILE B3076 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS B3081 " --> pdb=" O VAL B3077 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS B3084 " --> pdb=" O THR B3080 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU B3085 " --> pdb=" O CYS B3081 " (cutoff:3.500A) Processing helix chain 'B' and resid 3089 through 3099 removed outlier: 3.766A pdb=" N ALA B3093 " --> pdb=" O MET B3089 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B3095 " --> pdb=" O MET B3091 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS B3096 " --> pdb=" O ALA B3092 " (cutoff:3.500A) Processing helix chain 'B' and resid 3284 through 3299 removed outlier: 3.524A pdb=" N PHE B3291 " --> pdb=" O LEU B3287 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B3294 " --> pdb=" O LEU B3290 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B3296 " --> pdb=" O LEU B3292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP B3298 " --> pdb=" O ALA B3294 " (cutoff:3.500A) Processing helix chain 'B' and resid 3322 through 3327 Processing helix chain 'B' and resid 3334 through 3338 Processing helix chain 'B' and resid 3340 through 3344 Processing helix chain 'B' and resid 3557 through 3570 removed outlier: 4.147A pdb=" N SER B3562 " --> pdb=" O ALA B3558 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B3563 " --> pdb=" O HIS B3559 " (cutoff:3.500A) Processing helix chain 'B' and resid 3570 through 3577 Processing helix chain 'B' and resid 3582 through 3602 removed outlier: 4.024A pdb=" N VAL B3586 " --> pdb=" O PRO B3582 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP B3588 " --> pdb=" O VAL B3584 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B3595 " --> pdb=" O SER B3591 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B3599 " --> pdb=" O SER B3595 " (cutoff:3.500A) Processing helix chain 'B' and resid 3602 through 3611 removed outlier: 4.845A pdb=" N LEU B3609 " --> pdb=" O PRO B3605 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B3610 " --> pdb=" O LEU B3606 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B3611 " --> pdb=" O LYS B3607 " (cutoff:3.500A) Processing helix chain 'B' and resid 3659 through 3692 removed outlier: 3.709A pdb=" N VAL B3664 " --> pdb=" O GLU B3660 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B3665 " --> pdb=" O ALA B3661 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B3666 " --> pdb=" O ARG B3662 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B3669 " --> pdb=" O LYS B3665 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B3673 " --> pdb=" O GLY B3669 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B3675 " --> pdb=" O LEU B3671 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B3679 " --> pdb=" O LEU B3675 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B3682 " --> pdb=" O MET B3678 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B3686 " --> pdb=" O LEU B3682 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B3689 " --> pdb=" O LEU B3685 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B3690 " --> pdb=" O LEU B3686 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP B3691 " --> pdb=" O ALA B3687 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B3692 " --> pdb=" O SER B3688 " (cutoff:3.500A) Processing helix chain 'B' and resid 3700 through 3709 removed outlier: 4.148A pdb=" N LYS B3706 " --> pdb=" O GLN B3702 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B3707 " --> pdb=" O SER B3703 " (cutoff:3.500A) Processing helix chain 'B' and resid 3709 through 3714 removed outlier: 3.761A pdb=" N ALA B3713 " --> pdb=" O LEU B3709 " (cutoff:3.500A) Processing helix chain 'B' and resid 3725 through 3730 removed outlier: 3.630A pdb=" N VAL B3730 " --> pdb=" O MET B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3832 through 3840 removed outlier: 4.053A pdb=" N GLN B3838 " --> pdb=" O LEU B3834 " (cutoff:3.500A) Processing helix chain 'B' and resid 3893 through 3897 removed outlier: 3.915A pdb=" N LEU B3897 " --> pdb=" O SER B3894 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3918 removed outlier: 3.560A pdb=" N SER B3904 " --> pdb=" O PRO B3900 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B3905 " --> pdb=" O LEU B3901 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B3908 " --> pdb=" O SER B3904 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B3912 " --> pdb=" O LEU B3908 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA B3915 " --> pdb=" O ALA B3911 " (cutoff:3.500A) Processing helix chain 'B' and resid 3918 through 3923 removed outlier: 3.624A pdb=" N TRP B3922 " --> pdb=" O GLU B3918 " (cutoff:3.500A) Processing helix chain 'B' and resid 3939 through 3969 removed outlier: 4.073A pdb=" N ALA B3947 " --> pdb=" O ALA B3943 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B3949 " --> pdb=" O THR B3945 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B3950 " --> pdb=" O ALA B3946 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B3951 " --> pdb=" O ALA B3947 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B3954 " --> pdb=" O LEU B3950 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP B3960 " --> pdb=" O LEU B3956 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG B3961 " --> pdb=" O GLY B3957 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY B3969 " --> pdb=" O ARG B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3977 through 4005 removed outlier: 3.932A pdb=" N ALA B3981 " --> pdb=" O PHE B3977 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B3986 " --> pdb=" O GLN B3982 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B3990 " --> pdb=" O ALA B3986 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER B3993 " --> pdb=" O GLY B3989 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B3994 " --> pdb=" O LEU B3990 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B3999 " --> pdb=" O LEU B3995 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B4002 " --> pdb=" O LEU B3998 " (cutoff:3.500A) Processing helix chain 'B' and resid 4013 through 4038 removed outlier: 3.683A pdb=" N LYS B4017 " --> pdb=" O SER B4013 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B4019 " --> pdb=" O PHE B4015 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B4022 " --> pdb=" O THR B4018 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B4023 " --> pdb=" O LEU B4019 " (cutoff:3.500A) Proline residue: B4024 - end of helix removed outlier: 4.330A pdb=" N GLY B4028 " --> pdb=" O PRO B4024 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B4030 " --> pdb=" O LEU B4026 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY B4032 " --> pdb=" O GLY B4028 " (cutoff:3.500A) Processing helix chain 'B' and resid 4084 through 4089 Processing helix chain 'B' and resid 4096 through 4100 Processing helix chain 'B' and resid 4101 through 4118 removed outlier: 4.449A pdb=" N ILE B4105 " --> pdb=" O LEU B4101 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B4106 " --> pdb=" O GLY B4102 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B4107 " --> pdb=" O ALA B4103 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B4116 " --> pdb=" O ALA B4112 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 242 removed outlier: 3.755A pdb=" N VAL F 225 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE F 230 " --> pdb=" O THR F 226 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET F 242 " --> pdb=" O THR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 259 removed outlier: 3.687A pdb=" N MET F 252 " --> pdb=" O TYR F 248 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER F 254 " --> pdb=" O THR F 250 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU F 258 " --> pdb=" O SER F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 334 through 338 removed outlier: 3.722A pdb=" N LEU F 337 " --> pdb=" O PRO F 334 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG F 338 " --> pdb=" O GLN F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 338' Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.826A pdb=" N GLU F 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 412 removed outlier: 4.126A pdb=" N ALA F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN F 405 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN F 412 " --> pdb=" O SER F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 496 removed outlier: 4.151A pdb=" N ALA F 474 " --> pdb=" O ASP F 470 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE F 478 " --> pdb=" O ALA F 474 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE F 479 " --> pdb=" O ALA F 475 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 489 " --> pdb=" O PHE F 485 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 490 " --> pdb=" O TYR F 486 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 496 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 528 removed outlier: 3.552A pdb=" N VAL F 515 " --> pdb=" O ASP F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 548 through 571 removed outlier: 4.262A pdb=" N TRP F 554 " --> pdb=" O HIS F 550 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN F 555 " --> pdb=" O LEU F 551 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE F 556 " --> pdb=" O ALA F 552 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN F 557 " --> pdb=" O TYR F 553 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA F 563 " --> pdb=" O ASN F 559 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP F 570 " --> pdb=" O VAL F 566 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE F 571 " --> pdb=" O PHE F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 576 Processing helix chain 'F' and resid 580 through 620 removed outlier: 4.175A pdb=" N LEU F 586 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET F 590 " --> pdb=" O LEU F 586 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA F 594 " --> pdb=" O MET F 590 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS F 595 " --> pdb=" O SER F 591 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP F 596 " --> pdb=" O ARG F 592 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY F 599 " --> pdb=" O LYS F 595 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET F 603 " --> pdb=" O GLY F 599 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE F 605 " --> pdb=" O ALA F 601 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE F 607 " --> pdb=" O MET F 603 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN F 613 " --> pdb=" O LEU F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 627 Processing helix chain 'F' and resid 628 through 642 removed outlier: 3.878A pdb=" N PHE F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 635 " --> pdb=" O GLU F 631 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN F 636 " --> pdb=" O CYS F 632 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 637 " --> pdb=" O ILE F 633 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 638 " --> pdb=" O PHE F 634 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 639 " --> pdb=" O THR F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 653 Processing helix chain 'F' and resid 655 through 671 removed outlier: 3.554A pdb=" N ILE F 659 " --> pdb=" O VAL F 655 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE F 667 " --> pdb=" O THR F 663 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 692 removed outlier: 3.961A pdb=" N PHE F 676 " --> pdb=" O LEU F 672 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE F 680 " --> pdb=" O PHE F 676 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER F 689 " --> pdb=" O SER F 685 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 242 removed outlier: 3.754A pdb=" N VAL G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE G 230 " --> pdb=" O THR G 226 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET G 242 " --> pdb=" O THR G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 259 removed outlier: 3.687A pdb=" N MET G 252 " --> pdb=" O TYR G 248 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER G 254 " --> pdb=" O THR G 250 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE G 257 " --> pdb=" O MET G 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU G 258 " --> pdb=" O SER G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 286 through 291 Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 334 through 338 removed outlier: 3.723A pdb=" N LEU G 337 " --> pdb=" O PRO G 334 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG G 338 " --> pdb=" O GLN G 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 334 through 338' Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.826A pdb=" N GLU G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 412 removed outlier: 4.125A pdb=" N ALA G 404 " --> pdb=" O GLU G 400 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN G 405 " --> pdb=" O GLU G 401 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN G 412 " --> pdb=" O SER G 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 468 through 496 removed outlier: 3.868A pdb=" N ILE G 478 " --> pdb=" O ALA G 474 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE G 479 " --> pdb=" O ALA G 475 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 489 " --> pdb=" O PHE G 485 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU G 490 " --> pdb=" O TYR G 486 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG G 496 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 528 removed outlier: 3.552A pdb=" N VAL G 515 " --> pdb=" O ASP G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 539 Processing helix chain 'G' and resid 548 through 571 removed outlier: 4.263A pdb=" N TRP G 554 " --> pdb=" O HIS G 550 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN G 555 " --> pdb=" O LEU G 551 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE G 556 " --> pdb=" O ALA G 552 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN G 557 " --> pdb=" O TYR G 553 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA G 563 " --> pdb=" O ASN G 559 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL G 566 " --> pdb=" O ALA G 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP G 570 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE G 571 " --> pdb=" O PHE G 567 " (cutoff:3.500A) Processing helix chain 'G' and resid 572 through 576 Processing helix chain 'G' and resid 580 through 620 removed outlier: 4.174A pdb=" N LEU G 586 " --> pdb=" O THR G 582 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET G 590 " --> pdb=" O LEU G 586 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA G 594 " --> pdb=" O MET G 590 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS G 595 " --> pdb=" O SER G 591 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP G 596 " --> pdb=" O ARG G 592 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY G 599 " --> pdb=" O LYS G 595 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET G 603 " --> pdb=" O GLY G 599 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G 605 " --> pdb=" O ALA G 601 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE G 607 " --> pdb=" O MET G 603 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN G 613 " --> pdb=" O LEU G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 623 through 627 Processing helix chain 'G' and resid 628 through 642 removed outlier: 3.878A pdb=" N PHE G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR G 635 " --> pdb=" O GLU G 631 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN G 636 " --> pdb=" O CYS G 632 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE G 637 " --> pdb=" O ILE G 633 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG G 638 " --> pdb=" O PHE G 634 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE G 639 " --> pdb=" O THR G 635 " (cutoff:3.500A) Processing helix chain 'G' and resid 648 through 653 Processing helix chain 'G' and resid 655 through 671 removed outlier: 3.553A pdb=" N ILE G 659 " --> pdb=" O VAL G 655 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE G 667 " --> pdb=" O THR G 663 " (cutoff:3.500A) Processing helix chain 'G' and resid 671 through 696 removed outlier: 3.961A pdb=" N PHE G 676 " --> pdb=" O LEU G 672 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE G 680 " --> pdb=" O PHE G 676 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER G 689 " --> pdb=" O SER G 685 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 322 through 325 removed outlier: 4.037A pdb=" N LEU A 324 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA A 421 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA3, first strand: chain 'A' and resid 440 through 442 Processing sheet with id=AA4, first strand: chain 'B' and resid 3138 through 3139 Processing sheet with id=AA5, first strand: chain 'B' and resid 3142 through 3144 removed outlier: 3.608A pdb=" N LEU B3142 " --> pdb=" O SER B3149 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B3147 " --> pdb=" O GLY B3144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 3748 through 3749 removed outlier: 3.698A pdb=" N ARG B3748 " --> pdb=" O GLU B3853 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B3853 " --> pdb=" O ARG B3748 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B3852 " --> pdb=" O LEU B3869 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B3869 " --> pdb=" O LEU B3852 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B3858 " --> pdb=" O LEU B3863 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU B3863 " --> pdb=" O SER B3858 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 393 through 394 removed outlier: 3.869A pdb=" N ALA F 421 " --> pdb=" O LEU F 324 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE F 426 " --> pdb=" O VAL F 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 379 through 380 Processing sheet with id=AA9, first strand: chain 'G' and resid 393 through 394 removed outlier: 3.869A pdb=" N ALA G 421 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE G 426 " --> pdb=" O VAL G 439 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 379 through 380 647 hydrogen bonds defined for protein. 1818 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: 4.63 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3031 1.33 - 1.45: 3883 1.45 - 1.57: 8460 1.57 - 1.69: 1 1.69 - 1.81: 93 Bond restraints: 15468 Sorted by residual: bond pdb=" CB ASN G 430 " pdb=" CG ASN G 430 " ideal model delta sigma weight residual 1.516 1.434 0.082 2.50e-02 1.60e+03 1.08e+01 bond pdb=" CB LYS F 572 " pdb=" CG LYS F 572 " ideal model delta sigma weight residual 1.520 1.433 0.087 3.00e-02 1.11e+03 8.37e+00 bond pdb=" CA SER G 307 " pdb=" CB SER G 307 " ideal model delta sigma weight residual 1.526 1.480 0.046 1.70e-02 3.46e+03 7.21e+00 bond pdb=" N SER B3976 " pdb=" CA SER B3976 " ideal model delta sigma weight residual 1.463 1.439 0.024 1.08e-02 8.57e+03 4.97e+00 bond pdb=" CB VAL F 443 " pdb=" CG1 VAL F 443 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.91e+00 ... (remaining 15463 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.33: 147 104.33 - 111.81: 6844 111.81 - 119.28: 5474 119.28 - 126.75: 8430 126.75 - 134.23: 214 Bond angle restraints: 21109 Sorted by residual: angle pdb=" N SER B3976 " pdb=" CA SER B3976 " pdb=" C SER B3976 " ideal model delta sigma weight residual 111.04 123.85 -12.81 1.55e+00 4.16e-01 6.83e+01 angle pdb=" N VAL B3912 " pdb=" CA VAL B3912 " pdb=" C VAL B3912 " ideal model delta sigma weight residual 112.96 106.74 6.22 1.00e+00 1.00e+00 3.87e+01 angle pdb=" C ALA B4022 " pdb=" N LEU B4023 " pdb=" CA LEU B4023 " ideal model delta sigma weight residual 120.06 126.70 -6.64 1.19e+00 7.06e-01 3.11e+01 angle pdb=" CA LEU G 460 " pdb=" CB LEU G 460 " pdb=" CG LEU G 460 " ideal model delta sigma weight residual 116.30 134.23 -17.93 3.50e+00 8.16e-02 2.62e+01 angle pdb=" CA LEU F 500 " pdb=" CB LEU F 500 " pdb=" CG LEU F 500 " ideal model delta sigma weight residual 116.30 133.48 -17.18 3.50e+00 8.16e-02 2.41e+01 ... (remaining 21104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 8282 16.08 - 32.17: 495 32.17 - 48.25: 127 48.25 - 64.33: 11 64.33 - 80.41: 15 Dihedral angle restraints: 8930 sinusoidal: 2839 harmonic: 6091 Sorted by residual: dihedral pdb=" CA ALA B3306 " pdb=" C ALA B3306 " pdb=" N TYR B3307 " pdb=" CA TYR B3307 " ideal model delta harmonic sigma weight residual 180.00 129.21 50.79 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA ILE G 577 " pdb=" C ILE G 577 " pdb=" N ASN G 578 " pdb=" CA ASN G 578 " ideal model delta harmonic sigma weight residual 180.00 135.16 44.84 0 5.00e+00 4.00e-02 8.04e+01 dihedral pdb=" CA ILE F 577 " pdb=" C ILE F 577 " pdb=" N ASN F 578 " pdb=" CA ASN F 578 " ideal model delta harmonic sigma weight residual 180.00 135.17 44.83 0 5.00e+00 4.00e-02 8.04e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1998 0.069 - 0.138: 429 0.138 - 0.207: 38 0.207 - 0.276: 9 0.276 - 0.345: 6 Chirality restraints: 2480 Sorted by residual: chirality pdb=" CG LEU F 224 " pdb=" CB LEU F 224 " pdb=" CD1 LEU F 224 " pdb=" CD2 LEU F 224 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE F 577 " pdb=" CA ILE F 577 " pdb=" CG1 ILE F 577 " pdb=" CG2 ILE F 577 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CB ILE G 577 " pdb=" CA ILE G 577 " pdb=" CG1 ILE G 577 " pdb=" CG2 ILE G 577 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2477 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 318 " 0.058 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO F 319 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO F 319 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 319 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 576 " 0.039 2.00e-02 2.50e+03 2.43e-02 1.03e+01 pdb=" CG PHE F 576 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE F 576 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE F 576 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE F 576 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE F 576 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE F 576 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 646 " 0.017 2.00e-02 2.50e+03 2.32e-02 9.43e+00 pdb=" CG PHE A 646 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 646 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 646 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 646 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 646 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 646 " -0.005 2.00e-02 2.50e+03 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1692 2.74 - 3.28: 13997 3.28 - 3.82: 23397 3.82 - 4.36: 26526 4.36 - 4.90: 45027 Nonbonded interactions: 110639 Sorted by model distance: nonbonded pdb=" OD1 ASP F 624 " pdb=" OH TYR G 247 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR G 227 " pdb=" O VAL G 569 " model vdw 2.247 2.440 nonbonded pdb=" O LEU G 291 " pdb=" OG SER G 307 " model vdw 2.282 2.440 nonbonded pdb=" OE1 GLN B3702 " pdb=" NZ LYS B3706 " model vdw 2.284 2.520 nonbonded pdb=" NH2 ARG B3269 " pdb=" O SER B3273 " model vdw 2.304 2.520 ... (remaining 110634 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' selection = (chain 'F' and ((resid 219 through 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 or (resid 227 through 239 and (name N or name CA or \ name C or name O or name CB )) or resid 240 or (resid 241 through 260 and (name \ N or name CA or name C or name O or name CB )) or resid 261 or (resid 262 throu \ gh 284 and (name N or name CA or name C or name O or name CB )) or resid 285 or \ (resid 286 through 289 and (name N or name CA or name C or name O or name CB )) \ or resid 290 or (resid 291 and (name N or name CA or name C or name O or name CB \ )) or (resid 313 through 316 and (name N or name CA or name C or name O or name \ CB )) or resid 317 or (resid 318 through 325 and (name N or name CA or name C o \ r name O or name CB )) or resid 326 or (resid 327 through 328 and (name N or nam \ e CA or name C or name O or name CB )) or resid 329 or (resid 330 through 358 an \ d (name N or name CA or name C or name O or name CB )) or resid 359 or (resid 36 \ 0 through 362 and (name N or name CA or name C or name O or name CB )) or resid \ 363 or (resid 364 through 375 and (name N or name CA or name C or name O or name \ CB )) or resid 376 or (resid 377 through 380 and (name N or name CA or name C o \ r name O or name CB )) or resid 381 or (resid 382 through 387 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 388 through 417 and (name N or \ name CA or name C or name O or name CB )) or resid 418 or (resid 419 through 448 \ and (name N or name CA or name C or name O or name CB )) or resid 449 through 4 \ 50 or (resid 451 through 463 and (name N or name CA or name C or name O or name \ CB )) or (resid 471 through 522 and (name N or name CA or name C or name O or na \ me CB )) or resid 523 or (resid 524 through 531 and (name N or name CA or name C \ or name O or name CB )) or resid 532 or (resid 533 through 580 and (name N or n \ ame CA or name C or name O or name CB )) or resid 581 through 583 or (resid 584 \ and (name N or name CA or name C or name O or name CB )) or resid 585 through 58 \ 8 or (resid 589 and (name N or name CA or name C or name O or name CB )) or resi \ d 590 through 595 or (resid 596 and (name N or name CA or name C or name O or na \ me CB )) or resid 597 through 623 or (resid 624 through 625 and (name N or name \ CA or name C or name O or name CB )) or resid 626 through 682 or (resid 683 and \ (name N or name CA or name C or name O or name CB )) or resid 684 through 687 or \ (resid 688 and (name N or name CA or name C or name O or name CB )) or resid 68 \ 9 through 694)) selection = (chain 'G' and ((resid 219 through 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 or (resid 227 through 239 and (name N or name CA or \ name C or name O or name CB )) or resid 240 or (resid 241 through 260 and (name \ N or name CA or name C or name O or name CB )) or resid 261 or (resid 262 throu \ gh 284 and (name N or name CA or name C or name O or name CB )) or resid 285 or \ (resid 286 through 289 and (name N or name CA or name C or name O or name CB )) \ or resid 290 or (resid 291 and (name N or name CA or name C or name O or name CB \ )) or (resid 313 through 316 and (name N or name CA or name C or name O or name \ CB )) or (resid 317 through 325 and (name N or name CA or name C or name O or n \ ame CB )) or resid 326 or (resid 327 through 328 and (name N or name CA or name \ C or name O or name CB )) or resid 329 or (resid 330 through 358 and (name N or \ name CA or name C or name O or name CB )) or resid 359 or (resid 360 through 362 \ and (name N or name CA or name C or name O or name CB )) or resid 363 or (resid \ 364 through 375 and (name N or name CA or name C or name O or name CB )) or res \ id 376 or (resid 377 through 380 and (name N or name CA or name C or name O or n \ ame CB )) or resid 381 or (resid 382 through 387 and (name N or name CA or name \ C or name O or name CB )) or (resid 388 through 417 and (name N or name CA or na \ me C or name O or name CB )) or resid 418 or (resid 419 through 448 and (name N \ or name CA or name C or name O or name CB )) or resid 449 through 450 or (resid \ 451 through 463 and (name N or name CA or name C or name O or name CB )) or (res \ id 471 through 522 and (name N or name CA or name C or name O or name CB )) or r \ esid 523 or (resid 524 through 531 and (name N or name CA or name C or name O or \ name CB )) or resid 532 or (resid 533 through 580 and (name N or name CA or nam \ e C or name O or name CB )) or resid 581 through 583 or (resid 584 and (name N o \ r name CA or name C or name O or name CB )) or resid 585 through 588 or (resid 5 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 590 through \ 595 or (resid 596 and (name N or name CA or name C or name O or name CB )) or r \ esid 597 through 623 or (resid 624 through 625 and (name N or name CA or name C \ or name O or name CB )) or resid 626 through 682 or (resid 683 and (name N or na \ me CA or name C or name O or name CB )) or resid 684 through 687 or (resid 688 a \ nd (name N or name CA or name C or name O or name CB )) or resid 689 through 694 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 9812 2.51 5 N 2574 2.21 5 O 2695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.980 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.130 Process input model: 40.120 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.087 15468 Z= 0.545 Angle : 1.202 17.928 21109 Z= 0.627 Chirality : 0.059 0.345 2480 Planarity : 0.007 0.089 2692 Dihedral : 12.369 80.415 4976 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.18 % Favored : 90.67 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -6.41 (0.12), residues: 2058 helix: -4.75 (0.06), residues: 998 sheet: -2.42 (0.35), residues: 162 loop : -3.89 (0.16), residues: 898 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 433 time to evaluate : 2.000 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 447 average time/residue: 0.2746 time to fit residues: 177.4558 Evaluate side-chains 223 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 220 time to evaluate : 1.925 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1307 time to fit residues: 3.2030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 chunk 105 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3295 ASN B3729 HIS F 405 GLN F 432 ASN F 434 ASN F 613 GLN ** F 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 ASN ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 555 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 15468 Z= 0.232 Angle : 0.792 13.756 21109 Z= 0.412 Chirality : 0.046 0.273 2480 Planarity : 0.005 0.075 2692 Dihedral : 6.503 39.869 2225 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -4.56 (0.15), residues: 2058 helix: -2.83 (0.12), residues: 1015 sheet: -2.11 (0.34), residues: 176 loop : -3.35 (0.18), residues: 867 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 242 time to evaluate : 1.812 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: 53 outliers final: 29 residues processed: 274 average time/residue: 0.2618 time to fit residues: 108.4360 Evaluate side-chains 231 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 202 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1380 time to fit residues: 9.9496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 156 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 51 optimal weight: 40.0000 chunk 188 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 456 GLN ** G 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15468 Z= 0.171 Angle : 0.693 11.967 21109 Z= 0.350 Chirality : 0.043 0.206 2480 Planarity : 0.004 0.049 2692 Dihedral : 5.873 36.741 2225 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.71 (0.16), residues: 2058 helix: -1.96 (0.14), residues: 1019 sheet: -1.66 (0.37), residues: 165 loop : -3.19 (0.19), residues: 874 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 222 time to evaluate : 1.983 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: 42 outliers final: 15 residues processed: 254 average time/residue: 0.2548 time to fit residues: 97.4352 Evaluate side-chains 205 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1294 time to fit residues: 6.0116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 89 optimal weight: 8.9990 chunk 126 optimal weight: 0.5980 chunk 188 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 179 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B3096 HIS ** B3702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN F 405 GLN F 613 GLN ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 456 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 15468 Z= 0.247 Angle : 0.731 12.452 21109 Z= 0.364 Chirality : 0.044 0.193 2480 Planarity : 0.004 0.043 2692 Dihedral : 5.475 35.713 2225 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.17), residues: 2058 helix: -1.14 (0.15), residues: 1011 sheet: -1.45 (0.37), residues: 177 loop : -2.96 (0.20), residues: 870 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 193 time to evaluate : 2.047 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: 48 outliers final: 26 residues processed: 227 average time/residue: 0.2544 time to fit residues: 88.4588 Evaluate side-chains 192 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1624 time to fit residues: 9.7528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 50 optimal weight: 0.0770 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3295 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 580 ASN F 674 ASN ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15468 Z= 0.178 Angle : 0.677 12.110 21109 Z= 0.336 Chirality : 0.043 0.184 2480 Planarity : 0.003 0.041 2692 Dihedral : 5.234 35.338 2225 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.18), residues: 2058 helix: -0.69 (0.16), residues: 1003 sheet: -1.45 (0.38), residues: 177 loop : -2.78 (0.20), residues: 878 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 8 residues processed: 194 average time/residue: 0.2569 time to fit residues: 75.8820 Evaluate side-chains 165 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 157 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1442 time to fit residues: 4.6023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 30.0000 chunk 200 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B3707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 547 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 GLN ** F 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 15468 Z= 0.263 Angle : 0.721 11.912 21109 Z= 0.366 Chirality : 0.045 0.183 2480 Planarity : 0.004 0.040 2692 Dihedral : 5.306 33.216 2225 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.18), residues: 2058 helix: -0.45 (0.16), residues: 1033 sheet: -1.12 (0.41), residues: 167 loop : -2.79 (0.19), residues: 858 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 151 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 182 average time/residue: 0.2515 time to fit residues: 71.0017 Evaluate side-chains 163 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.881 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1802 time to fit residues: 9.0363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 114 optimal weight: 0.4980 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 199 optimal weight: 0.0670 chunk 124 optimal weight: 0.0060 chunk 121 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.9138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 15468 Z= 0.144 Angle : 0.659 12.809 21109 Z= 0.323 Chirality : 0.043 0.196 2480 Planarity : 0.003 0.034 2692 Dihedral : 4.944 33.503 2225 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.18), residues: 2058 helix: -0.15 (0.16), residues: 1031 sheet: -0.94 (0.40), residues: 175 loop : -2.65 (0.20), residues: 852 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 169 average time/residue: 0.2568 time to fit residues: 67.2556 Evaluate side-chains 142 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1453 time to fit residues: 3.9502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.0010 chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 60 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 98 optimal weight: 0.0870 chunk 18 optimal weight: 40.0000 chunk 156 optimal weight: 2.9990 overall best weight: 1.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 GLN ** F 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.7339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 15468 Z= 0.145 Angle : 0.659 11.649 21109 Z= 0.322 Chirality : 0.043 0.214 2480 Planarity : 0.003 0.033 2692 Dihedral : 4.794 33.271 2225 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.18), residues: 2058 helix: 0.06 (0.16), residues: 1032 sheet: -1.01 (0.40), residues: 181 loop : -2.56 (0.20), residues: 845 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 159 average time/residue: 0.2496 time to fit residues: 61.9541 Evaluate side-chains 138 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 1.844 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1407 time to fit residues: 2.9662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 0.9990 chunk 191 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 80 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 168 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 580 ASN ** F 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.7512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 15468 Z= 0.141 Angle : 0.665 13.554 21109 Z= 0.323 Chirality : 0.043 0.190 2480 Planarity : 0.003 0.035 2692 Dihedral : 4.647 32.797 2225 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.19), residues: 2058 helix: 0.17 (0.17), residues: 1031 sheet: -0.87 (0.40), residues: 181 loop : -2.47 (0.20), residues: 846 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 157 average time/residue: 0.2541 time to fit residues: 61.9680 Evaluate side-chains 143 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.938 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1376 time to fit residues: 2.6999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 17 optimal weight: 50.0000 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 613 GLN ** F 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.8187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 15468 Z= 0.249 Angle : 0.737 11.624 21109 Z= 0.372 Chirality : 0.045 0.196 2480 Planarity : 0.004 0.033 2692 Dihedral : 4.994 33.072 2225 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.56 (0.19), residues: 2058 helix: 0.14 (0.16), residues: 1048 sheet: -1.02 (0.38), residues: 198 loop : -2.63 (0.21), residues: 812 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 143 average time/residue: 0.2542 time to fit residues: 57.4910 Evaluate side-chains 135 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.977 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1447 time to fit residues: 3.6665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 9.9990 chunk 50 optimal weight: 0.0970 chunk 151 optimal weight: 0.9990 chunk 24 optimal weight: 50.0000 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 168 optimal weight: 0.9980 chunk 20 optimal weight: 30.0000 chunk 30 optimal weight: 0.6980 chunk 144 optimal weight: 9.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 613 GLN ** F 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.083983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.073049 restraints weight = 88022.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.074272 restraints weight = 55568.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.075110 restraints weight = 39349.598| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.8213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 15468 Z= 0.152 Angle : 0.689 14.206 21109 Z= 0.331 Chirality : 0.044 0.217 2480 Planarity : 0.003 0.041 2692 Dihedral : 4.717 31.688 2225 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 2058 helix: 0.32 (0.17), residues: 1037 sheet: -0.78 (0.39), residues: 195 loop : -2.48 (0.21), residues: 826 =============================================================================== Job complete usr+sys time: 2718.33 seconds wall clock time: 50 minutes 10.49 seconds (3010.49 seconds total)