Starting phenix.real_space_refine on Sat Mar 16 16:34:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a70_6991/03_2024/6a70_6991.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a70_6991/03_2024/6a70_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_6991/03_2024/6a70_6991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a70_6991/03_2024/6a70_6991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a70_6991/03_2024/6a70_6991.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a70_6991/03_2024/6a70_6991.pdb" } resolution = 3.6 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= 0.001 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 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. 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-5265/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: 8.06, per 1000 atoms: 0.53 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: 5.16 Conformation dependent library (CDL) restraints added in 3.0 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: 1.66 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: 4.40 Time building geometry restraints manager: 5.68 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 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.100 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.500 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5889 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 % Allowed : 7.62 % Favored : 91.09 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP B3726 HIS 0.016 0.003 HIS B3864 PHE 0.053 0.005 PHE A 646 TYR 0.034 0.004 TYR B3857 ARG 0.020 0.002 ARG F 322 *********************** 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 : 1.698 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 REVERT: B 3978 ASP cc_start: 0.4152 (p0) cc_final: 0.3803 (p0) REVERT: B 4043 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6994 (pt) REVERT: F 543 ASN cc_start: 0.7161 (t0) cc_final: 0.6567 (p0) REVERT: G 335 GLN cc_start: 0.7671 (mp-120) cc_final: 0.7300 (pm20) outliers start: 17 outliers final: 3 residues processed: 447 average time/residue: 0.2731 time to fit residues: 175.2813 Evaluate side-chains 227 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3686 LEU Chi-restraints excluded: chain B residue 4043 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 573 LEU 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: 10.0000 chunk 162 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3295 ASN F 405 GLN F 432 ASN F 434 ASN F 613 GLN F 681 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.3704 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= 0.229 Angle : 0.788 13.956 21109 Z= 0.407 Chirality : 0.046 0.259 2480 Planarity : 0.005 0.068 2692 Dihedral : 6.695 54.964 2233 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.58 % Favored : 92.37 % Rotamer: Outliers : 3.92 % Allowed : 17.21 % Favored : 78.87 % 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: -4.53 (0.15), residues: 2058 helix: -2.81 (0.12), residues: 1014 sheet: -2.09 (0.34), residues: 176 loop : -3.34 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 380 HIS 0.006 0.001 HIS G 379 PHE 0.029 0.002 PHE A 646 TYR 0.026 0.002 TYR F 616 ARG 0.006 0.001 ARG F 322 *********************** 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 297 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 245 time to evaluate : 1.530 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 590 MET cc_start: 0.5372 (ppp) cc_final: 0.5108 (ppp) REVERT: B 3599 SER cc_start: 0.6494 (t) cc_final: 0.5902 (p) REVERT: B 4043 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7066 (pt) REVERT: B 4106 LEU cc_start: 0.7292 (mt) cc_final: 0.7031 (mp) REVERT: F 284 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: F 543 ASN cc_start: 0.7174 (t0) cc_final: 0.6662 (p0) REVERT: F 583 MET cc_start: 0.6887 (mmt) cc_final: 0.6529 (mmm) REVERT: G 335 GLN cc_start: 0.7772 (mp-120) cc_final: 0.7342 (pm20) outliers start: 52 outliers final: 26 residues processed: 277 average time/residue: 0.2533 time to fit residues: 106.0785 Evaluate side-chains 237 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 209 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 3077 VAL Chi-restraints excluded: chain B residue 3266 ILE Chi-restraints excluded: chain B residue 3585 SER Chi-restraints excluded: chain B residue 3709 LEU Chi-restraints excluded: chain B residue 3730 VAL Chi-restraints excluded: chain B residue 3797 TYR Chi-restraints excluded: chain B residue 3802 LEU Chi-restraints excluded: chain B residue 3944 LEU Chi-restraints excluded: chain B residue 4036 LEU Chi-restraints excluded: chain B residue 4043 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain F residue 593 CYS Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 625 ASP Chi-restraints excluded: chain F residue 655 VAL Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 579 PHE Chi-restraints excluded: chain G residue 633 ILE 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: 0.0980 chunk 156 optimal weight: 0.0980 chunk 128 optimal weight: 0.0010 chunk 51 optimal weight: 40.0000 chunk 188 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3729 HIS ** B3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 456 GLN G 501 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15468 Z= 0.159 Angle : 0.690 12.825 21109 Z= 0.344 Chirality : 0.043 0.210 2480 Planarity : 0.004 0.047 2692 Dihedral : 5.893 57.582 2231 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.60 % Allowed : 17.89 % Favored : 77.51 % 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: -3.63 (0.16), residues: 2058 helix: -1.88 (0.15), residues: 1013 sheet: -1.66 (0.38), residues: 163 loop : -3.16 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B4096 HIS 0.016 0.001 HIS G 501 PHE 0.029 0.002 PHE G 646 TYR 0.022 0.001 TYR F 660 ARG 0.005 0.000 ARG A 581 *********************** 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 288 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 227 time to evaluate : 1.710 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 REVERT: A 590 MET cc_start: 0.5479 (ppp) cc_final: 0.5247 (ppp) REVERT: B 3599 SER cc_start: 0.5908 (t) cc_final: 0.5233 (p) REVERT: B 4043 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7115 (pt) REVERT: F 486 TYR cc_start: 0.6139 (t80) cc_final: 0.5481 (t80) REVERT: F 543 ASN cc_start: 0.7065 (t0) cc_final: 0.6571 (p0) REVERT: G 335 GLN cc_start: 0.7732 (mp-120) cc_final: 0.7269 (pm20) REVERT: G 448 THR cc_start: 0.6878 (p) cc_final: 0.6650 (p) outliers start: 61 outliers final: 30 residues processed: 271 average time/residue: 0.2454 time to fit residues: 100.2684 Evaluate side-chains 223 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 192 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3077 VAL Chi-restraints excluded: chain B residue 3338 LEU Chi-restraints excluded: chain B residue 3341 LEU Chi-restraints excluded: chain B residue 3585 SER Chi-restraints excluded: chain B residue 3709 LEU Chi-restraints excluded: chain B residue 3797 TYR Chi-restraints excluded: chain B residue 3902 LEU Chi-restraints excluded: chain B residue 3912 VAL Chi-restraints excluded: chain B residue 3944 LEU Chi-restraints excluded: chain B residue 3978 ASP Chi-restraints excluded: chain B residue 4036 LEU Chi-restraints excluded: chain B residue 4043 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 625 ASP Chi-restraints excluded: chain F residue 655 VAL Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 676 PHE Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 245 ASN Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 556 ILE Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 579 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 20 optimal weight: 40.0000 chunk 89 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3955 GLN F 405 GLN F 560 ASN F 613 GLN ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 456 GLN G 560 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15468 Z= 0.205 Angle : 0.687 12.118 21109 Z= 0.340 Chirality : 0.043 0.204 2480 Planarity : 0.003 0.037 2692 Dihedral : 5.382 35.171 2229 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.83 % Allowed : 18.34 % Favored : 76.83 % 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: -2.85 (0.17), residues: 2058 helix: -1.12 (0.15), residues: 1010 sheet: -1.38 (0.40), residues: 165 loop : -2.91 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B3298 HIS 0.004 0.001 HIS G 498 PHE 0.026 0.002 PHE G 646 TYR 0.013 0.001 TYR G 392 ARG 0.008 0.001 ARG G 464 *********************** 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 268 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 204 time to evaluate : 1.935 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: A 590 MET cc_start: 0.5519 (ppp) cc_final: 0.5257 (ppp) REVERT: F 543 ASN cc_start: 0.7336 (t0) cc_final: 0.6851 (p0) REVERT: G 335 GLN cc_start: 0.7773 (mp-120) cc_final: 0.7333 (pm20) REVERT: G 461 LYS cc_start: 0.7775 (pttt) cc_final: 0.7165 (ptmm) REVERT: G 625 ASP cc_start: 0.6455 (t0) cc_final: 0.6237 (t0) outliers start: 64 outliers final: 40 residues processed: 246 average time/residue: 0.2451 time to fit residues: 91.9645 Evaluate side-chains 214 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 174 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 3077 VAL Chi-restraints excluded: chain B residue 3091 MET Chi-restraints excluded: chain B residue 3266 ILE Chi-restraints excluded: chain B residue 3282 THR Chi-restraints excluded: chain B residue 3327 LEU Chi-restraints excluded: chain B residue 3346 MET Chi-restraints excluded: chain B residue 3585 SER Chi-restraints excluded: chain B residue 3609 LEU Chi-restraints excluded: chain B residue 3797 TYR Chi-restraints excluded: chain B residue 3868 THR Chi-restraints excluded: chain B residue 3897 LEU Chi-restraints excluded: chain B residue 3902 LEU Chi-restraints excluded: chain B residue 3910 PHE Chi-restraints excluded: chain B residue 3912 VAL Chi-restraints excluded: chain B residue 3944 LEU Chi-restraints excluded: chain B residue 3978 ASP Chi-restraints excluded: chain B residue 4019 LEU Chi-restraints excluded: chain B residue 4036 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 514 ILE Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 625 ASP Chi-restraints excluded: chain F residue 655 VAL Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 556 ILE Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 579 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 2 optimal weight: 0.0170 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 0.0000 chunk 170 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 50 optimal weight: 50.0000 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3295 ASN B3702 GLN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 ASN F 613 GLN F 674 ASN ** G 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15468 Z= 0.155 Angle : 0.654 11.227 21109 Z= 0.319 Chirality : 0.042 0.168 2480 Planarity : 0.003 0.042 2692 Dihedral : 5.057 31.372 2227 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.23 % Allowed : 19.85 % Favored : 75.92 % 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: -2.44 (0.18), residues: 2058 helix: -0.69 (0.16), residues: 1014 sheet: -1.41 (0.38), residues: 177 loop : -2.81 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B3263 HIS 0.005 0.001 HIS G 498 PHE 0.025 0.001 PHE G 646 TYR 0.021 0.001 TYR F 486 ARG 0.015 0.001 ARG F 320 *********************** 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 244 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 188 time to evaluate : 1.721 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 590 MET cc_start: 0.5665 (ppp) cc_final: 0.5324 (ppp) REVERT: B 3825 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4826 (pp) REVERT: B 3975 THR cc_start: 0.5811 (OUTLIER) cc_final: 0.5570 (m) REVERT: F 543 ASN cc_start: 0.7559 (t0) cc_final: 0.7136 (p0) REVERT: G 335 GLN cc_start: 0.7683 (mp-120) cc_final: 0.7326 (pm20) outliers start: 56 outliers final: 44 residues processed: 229 average time/residue: 0.2299 time to fit residues: 81.8284 Evaluate side-chains 218 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 3077 VAL Chi-restraints excluded: chain B residue 3091 MET Chi-restraints excluded: chain B residue 3266 ILE Chi-restraints excluded: chain B residue 3282 THR Chi-restraints excluded: chain B residue 3302 VAL Chi-restraints excluded: chain B residue 3327 LEU Chi-restraints excluded: chain B residue 3338 LEU Chi-restraints excluded: chain B residue 3585 SER Chi-restraints excluded: chain B residue 3609 LEU Chi-restraints excluded: chain B residue 3709 LEU Chi-restraints excluded: chain B residue 3797 TYR Chi-restraints excluded: chain B residue 3802 LEU Chi-restraints excluded: chain B residue 3825 LEU Chi-restraints excluded: chain B residue 3902 LEU Chi-restraints excluded: chain B residue 3910 PHE Chi-restraints excluded: chain B residue 3912 VAL Chi-restraints excluded: chain B residue 3944 LEU Chi-restraints excluded: chain B residue 3975 THR Chi-restraints excluded: chain B residue 3978 ASP Chi-restraints excluded: chain B residue 4019 LEU Chi-restraints excluded: chain B residue 4117 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 514 ILE Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 625 ASP Chi-restraints excluded: chain F residue 646 PHE Chi-restraints excluded: chain F residue 655 VAL Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 556 ILE Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 579 PHE Chi-restraints excluded: chain G residue 583 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 49 optimal weight: 40.0000 chunk 200 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 16 optimal weight: 0.0570 chunk 66 optimal weight: 0.0170 chunk 105 optimal weight: 4.9990 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3838 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15468 Z= 0.154 Angle : 0.627 12.482 21109 Z= 0.307 Chirality : 0.042 0.153 2480 Planarity : 0.003 0.032 2692 Dihedral : 4.833 30.031 2227 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.13 % Allowed : 19.85 % Favored : 75.02 % 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: -2.02 (0.18), residues: 2058 helix: -0.27 (0.17), residues: 1009 sheet: -1.12 (0.39), residues: 175 loop : -2.72 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B3298 HIS 0.005 0.001 HIS B3695 PHE 0.029 0.001 PHE B3977 TYR 0.021 0.001 TYR F 486 ARG 0.004 0.000 ARG F 320 *********************** 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 244 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 176 time to evaluate : 1.648 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 590 MET cc_start: 0.5445 (ppp) cc_final: 0.5167 (ppp) REVERT: F 543 ASN cc_start: 0.7648 (t0) cc_final: 0.7192 (p0) REVERT: G 335 GLN cc_start: 0.7680 (mp-120) cc_final: 0.7307 (pm20) REVERT: G 448 THR cc_start: 0.6850 (p) cc_final: 0.6615 (p) outliers start: 68 outliers final: 53 residues processed: 224 average time/residue: 0.2231 time to fit residues: 77.8432 Evaluate side-chains 223 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 3077 VAL Chi-restraints excluded: chain B residue 3266 ILE Chi-restraints excluded: chain B residue 3282 THR Chi-restraints excluded: chain B residue 3327 LEU Chi-restraints excluded: chain B residue 3609 LEU Chi-restraints excluded: chain B residue 3679 LEU Chi-restraints excluded: chain B residue 3709 LEU Chi-restraints excluded: chain B residue 3797 TYR Chi-restraints excluded: chain B residue 3897 LEU Chi-restraints excluded: chain B residue 3902 LEU Chi-restraints excluded: chain B residue 3910 PHE Chi-restraints excluded: chain B residue 3912 VAL Chi-restraints excluded: chain B residue 3944 LEU Chi-restraints excluded: chain B residue 3975 THR Chi-restraints excluded: chain B residue 3976 SER Chi-restraints excluded: chain B residue 3978 ASP Chi-restraints excluded: chain B residue 4036 LEU Chi-restraints excluded: chain B residue 4105 ILE Chi-restraints excluded: chain B residue 4117 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 487 TYR Chi-restraints excluded: chain F residue 514 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 625 ASP Chi-restraints excluded: chain F residue 646 PHE Chi-restraints excluded: chain F residue 651 GLU Chi-restraints excluded: chain F residue 655 VAL Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 556 ILE Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 579 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 114 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 111 optimal weight: 30.0000 chunk 199 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3736 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15468 Z= 0.176 Angle : 0.647 12.674 21109 Z= 0.317 Chirality : 0.043 0.158 2480 Planarity : 0.003 0.033 2692 Dihedral : 4.736 29.166 2227 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.98 % Allowed : 20.30 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.18), residues: 2058 helix: 0.10 (0.17), residues: 1016 sheet: -0.96 (0.39), residues: 178 loop : -2.60 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B3298 HIS 0.004 0.001 HIS B3695 PHE 0.026 0.001 PHE G 646 TYR 0.019 0.001 TYR F 486 ARG 0.004 0.000 ARG G 322 *********************** 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 241 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 175 time to evaluate : 1.679 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: A 590 MET cc_start: 0.5453 (ppp) cc_final: 0.5155 (ppp) REVERT: F 225 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7659 (p) REVERT: F 510 LEU cc_start: 0.7541 (tt) cc_final: 0.7232 (tt) REVERT: G 335 GLN cc_start: 0.7728 (mp-120) cc_final: 0.7458 (pm20) REVERT: G 497 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7075 (mp) outliers start: 66 outliers final: 47 residues processed: 225 average time/residue: 0.2191 time to fit residues: 78.2697 Evaluate side-chains 215 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 166 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 3077 VAL Chi-restraints excluded: chain B residue 3091 MET Chi-restraints excluded: chain B residue 3266 ILE Chi-restraints excluded: chain B residue 3282 THR Chi-restraints excluded: chain B residue 3327 LEU Chi-restraints excluded: chain B residue 3338 LEU Chi-restraints excluded: chain B residue 3585 SER Chi-restraints excluded: chain B residue 3707 GLN Chi-restraints excluded: chain B residue 3709 LEU Chi-restraints excluded: chain B residue 3902 LEU Chi-restraints excluded: chain B residue 3910 PHE Chi-restraints excluded: chain B residue 3912 VAL Chi-restraints excluded: chain B residue 3944 LEU Chi-restraints excluded: chain B residue 3975 THR Chi-restraints excluded: chain B residue 3976 SER Chi-restraints excluded: chain B residue 3978 ASP Chi-restraints excluded: chain B residue 4036 LEU Chi-restraints excluded: chain B residue 4117 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 487 TYR Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 625 ASP Chi-restraints excluded: chain F residue 646 PHE Chi-restraints excluded: chain F residue 655 VAL Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 497 ILE Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 579 PHE Chi-restraints excluded: chain G residue 617 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.0470 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.7884 ------------------------------------------------------------------------------- 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: 0.6579 moved from start: 0.6855 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= 0.136 Angle : 0.628 11.596 21109 Z= 0.304 Chirality : 0.042 0.183 2480 Planarity : 0.003 0.031 2692 Dihedral : 4.577 28.452 2227 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.77 % Allowed : 21.74 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 2058 helix: 0.32 (0.17), residues: 1020 sheet: -0.77 (0.39), residues: 182 loop : -2.56 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B3795 HIS 0.004 0.001 HIS G 498 PHE 0.024 0.001 PHE B3977 TYR 0.020 0.001 TYR F 486 ARG 0.004 0.000 ARG G 322 *********************** 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 227 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 177 time to evaluate : 1.892 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: A 590 MET cc_start: 0.5446 (ppp) cc_final: 0.5178 (ppp) REVERT: F 225 VAL cc_start: 0.7943 (OUTLIER) cc_final: 0.7569 (p) REVERT: F 510 LEU cc_start: 0.7567 (tt) cc_final: 0.7331 (tt) REVERT: G 335 GLN cc_start: 0.7680 (mp-120) cc_final: 0.7453 (pm20) REVERT: G 448 THR cc_start: 0.6777 (p) cc_final: 0.6510 (p) REVERT: G 497 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7003 (mp) outliers start: 50 outliers final: 37 residues processed: 216 average time/residue: 0.2382 time to fit residues: 79.6690 Evaluate side-chains 201 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 3091 MET Chi-restraints excluded: chain B residue 3266 ILE Chi-restraints excluded: chain B residue 3327 LEU Chi-restraints excluded: chain B residue 3707 GLN Chi-restraints excluded: chain B residue 3709 LEU Chi-restraints excluded: chain B residue 3902 LEU Chi-restraints excluded: chain B residue 3910 PHE Chi-restraints excluded: chain B residue 3944 LEU Chi-restraints excluded: chain B residue 3965 ARG Chi-restraints excluded: chain B residue 3975 THR Chi-restraints excluded: chain B residue 3976 SER Chi-restraints excluded: chain B residue 3978 ASP Chi-restraints excluded: chain B residue 4117 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 625 ASP Chi-restraints excluded: chain F residue 646 PHE Chi-restraints excluded: chain F residue 655 VAL Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 691 LEU Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 497 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 572 LYS Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 579 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 1.9990 chunk 191 optimal weight: 0.1980 chunk 174 optimal weight: 0.0170 chunk 185 optimal weight: 7.9990 chunk 111 optimal weight: 30.0000 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 57 optimal weight: 0.0060 chunk 168 optimal weight: 0.1980 chunk 175 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 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: 0.6570 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15468 Z= 0.136 Angle : 0.636 11.467 21109 Z= 0.304 Chirality : 0.042 0.209 2480 Planarity : 0.003 0.037 2692 Dihedral : 4.456 26.787 2227 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.70 % Allowed : 21.89 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.19), residues: 2058 helix: 0.55 (0.17), residues: 1012 sheet: -0.65 (0.40), residues: 178 loop : -2.44 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B3795 HIS 0.004 0.001 HIS G 498 PHE 0.025 0.001 PHE G 646 TYR 0.019 0.001 TYR F 486 ARG 0.008 0.000 ARG B4007 *********************** 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 222 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 1.730 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: A 590 MET cc_start: 0.5631 (ppp) cc_final: 0.5312 (ppp) REVERT: F 225 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7579 (p) REVERT: F 273 LEU cc_start: 0.8358 (tp) cc_final: 0.7917 (tp) REVERT: F 510 LEU cc_start: 0.7537 (tt) cc_final: 0.7313 (tt) REVERT: G 335 GLN cc_start: 0.7734 (mp-120) cc_final: 0.7469 (pm20) REVERT: G 448 THR cc_start: 0.6610 (p) cc_final: 0.6367 (p) REVERT: G 497 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7061 (mp) outliers start: 49 outliers final: 39 residues processed: 208 average time/residue: 0.2508 time to fit residues: 81.2848 Evaluate side-chains 205 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 3091 MET Chi-restraints excluded: chain B residue 3266 ILE Chi-restraints excluded: chain B residue 3327 LEU Chi-restraints excluded: chain B residue 3338 LEU Chi-restraints excluded: chain B residue 3707 GLN Chi-restraints excluded: chain B residue 3709 LEU Chi-restraints excluded: chain B residue 3897 LEU Chi-restraints excluded: chain B residue 3902 LEU Chi-restraints excluded: chain B residue 3910 PHE Chi-restraints excluded: chain B residue 3944 LEU Chi-restraints excluded: chain B residue 3965 ARG Chi-restraints excluded: chain B residue 3975 THR Chi-restraints excluded: chain B residue 3976 SER Chi-restraints excluded: chain B residue 3978 ASP Chi-restraints excluded: chain B residue 4117 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 646 PHE Chi-restraints excluded: chain F residue 655 VAL Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 691 LEU Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 497 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 572 LYS Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 579 PHE Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain G residue 631 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 chunk 164 optimal weight: 0.0270 chunk 17 optimal weight: 30.0000 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 overall best weight: 2.5644 ------------------------------------------------------------------------------- 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: 0.6696 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15468 Z= 0.187 Angle : 0.662 10.820 21109 Z= 0.324 Chirality : 0.043 0.196 2480 Planarity : 0.003 0.046 2692 Dihedral : 4.565 28.459 2227 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.17 % Allowed : 22.19 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 2058 helix: 0.65 (0.17), residues: 1029 sheet: -0.61 (0.41), residues: 169 loop : -2.46 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B3298 HIS 0.004 0.001 HIS G 498 PHE 0.025 0.002 PHE G 646 TYR 0.023 0.001 TYR F 486 ARG 0.010 0.001 ARG G 464 ********************** 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 204 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 1.660 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: B 3091 MET cc_start: 0.3883 (OUTLIER) cc_final: 0.2687 (ttm) REVERT: F 225 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7660 (p) REVERT: G 335 GLN cc_start: 0.7741 (mp-120) cc_final: 0.7485 (pm20) REVERT: G 497 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7036 (mp) outliers start: 42 outliers final: 34 residues processed: 194 average time/residue: 0.2380 time to fit residues: 72.0104 Evaluate side-chains 197 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 3091 MET Chi-restraints excluded: chain B residue 3266 ILE Chi-restraints excluded: chain B residue 3327 LEU Chi-restraints excluded: chain B residue 3338 LEU Chi-restraints excluded: chain B residue 3707 GLN Chi-restraints excluded: chain B residue 3897 LEU Chi-restraints excluded: chain B residue 3902 LEU Chi-restraints excluded: chain B residue 3910 PHE Chi-restraints excluded: chain B residue 3944 LEU Chi-restraints excluded: chain B residue 3965 ARG Chi-restraints excluded: chain B residue 3976 SER Chi-restraints excluded: chain B residue 3978 ASP Chi-restraints excluded: chain B residue 4117 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 486 TYR Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 607 ILE Chi-restraints excluded: chain F residue 646 PHE Chi-restraints excluded: chain F residue 655 VAL Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 497 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 579 PHE Chi-restraints excluded: chain G residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 10.0000 chunk 50 optimal weight: 0.0470 chunk 151 optimal weight: 0.9980 chunk 24 optimal weight: 50.0000 chunk 45 optimal weight: 20.0000 chunk 164 optimal weight: 0.0270 chunk 68 optimal weight: 0.9980 chunk 168 optimal weight: 0.3980 chunk 20 optimal weight: 50.0000 chunk 30 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 525 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.086572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.075225 restraints weight = 88060.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.076475 restraints weight = 55884.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.077326 restraints weight = 39768.314| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.7525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15468 Z= 0.138 Angle : 0.657 14.204 21109 Z= 0.311 Chirality : 0.043 0.211 2480 Planarity : 0.003 0.032 2692 Dihedral : 4.391 25.872 2227 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.64 % Allowed : 22.57 % Favored : 74.79 % 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: -0.92 (0.19), residues: 2058 helix: 0.73 (0.17), residues: 1033 sheet: -0.55 (0.40), residues: 173 loop : -2.39 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B3795 HIS 0.004 0.001 HIS G 498 PHE 0.024 0.001 PHE G 646 TYR 0.021 0.001 TYR F 486 ARG 0.008 0.000 ARG B4007 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2882.67 seconds wall clock time: 52 minutes 40.04 seconds (3160.04 seconds total)