Starting phenix.real_space_refine on Tue Nov 21 01:03:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y81_6816/11_2023/5y81_6816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y81_6816/11_2023/5y81_6816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y81_6816/11_2023/5y81_6816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y81_6816/11_2023/5y81_6816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y81_6816/11_2023/5y81_6816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y81_6816/11_2023/5y81_6816.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6248 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 15775 2.51 5 N 4861 2.21 5 O 5044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 2641": "OE1" <-> "OE2" Residue "B ARG 2834": "NH1" <-> "NH2" Residue "B GLU 2854": "OE1" <-> "OE2" Residue "B ARG 2969": "NH1" <-> "NH2" Residue "B ARG 3066": "NH1" <-> "NH2" Residue "B ARG 3067": "NH1" <-> "NH2" Residue "B ARG 3236": "NH1" <-> "NH2" Residue "B ARG 3247": "NH1" <-> "NH2" Residue "B ARG 3318": "NH1" <-> "NH2" Residue "B GLU 3417": "OE1" <-> "OE2" Residue "B ARG 3424": "NH1" <-> "NH2" Residue "B ARG 3437": "NH1" <-> "NH2" Residue "B ARG 3438": "NH1" <-> "NH2" Residue "B ARG 3668": "NH1" <-> "NH2" Residue "B ARG 3731": "NH1" <-> "NH2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "F ARG 438": "NH1" <-> "NH2" Residue "F TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 25723 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 5937 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 590} Link IDs: {'PTRANS': 38, 'TRANS': 942} Chain breaks: 22 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 2323 Unresolved non-hydrogen angles: 2983 Unresolved non-hydrogen dihedrals: 1964 Unresolved non-hydrogen chiralities: 185 Planarities with less than four sites: {'GLN:plan1': 36, 'HIS:plan': 18, 'TYR:plan': 23, 'ASN:plan1': 41, 'TRP:plan': 14, 'ASP:plan': 34, 'PHE:plan': 39, 'GLU:plan': 46, 'ARG:plan': 45} Unresolved non-hydrogen planarities: 1389 Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 800 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 412 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 9, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 261 Chain: "D" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 1800 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 360} Link IDs: {'TRANS': 359} Chain breaks: 4 Unresolved non-hydrogen bonds: 720 Unresolved non-hydrogen angles: 1080 Unresolved non-hydrogen dihedrals: 360 Planarities with less than four sites: {'UNK:plan-1': 360} Unresolved non-hydrogen planarities: 360 Chain: "H" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 764 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 517 Unresolved non-hydrogen angles: 655 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 18, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 271 Chain: "A" Number of atoms: 10017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2007, 10017 Classifications: {'peptide': 2007} Incomplete info: {'truncation_to_alanine': 1858} Link IDs: {'PTRANS': 78, 'TRANS': 1928} Chain breaks: 73 Unresolved chain link angles: 78 Unresolved non-hydrogen bonds: 6723 Unresolved non-hydrogen angles: 8608 Unresolved non-hydrogen dihedrals: 5562 Unresolved non-hydrogen chiralities: 707 Planarities with less than four sites: {'GLN:plan1': 69, 'HIS:plan': 35, 'TYR:plan': 81, 'ASN:plan1': 118, 'TRP:plan': 13, 'ASP:plan': 90, 'PHE:plan': 121, 'GLU:plan': 122, 'ARG:plan': 81} Unresolved non-hydrogen planarities: 3378 Chain: "F" Number of atoms: 3334 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3323 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 421, 3323 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3385 Chain: "G" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2729 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 332} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 342 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG F 489 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 489 " occ=0.50 Time building chain proxies: 16.14, per 1000 atoms: 0.63 Number of scatterers: 25723 At special positions: 0 Unit cell: (166.4, 231.4, 166.4, 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 43 16.00 O 5044 8.00 N 4861 7.00 C 15775 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: 10.90 Conformation dependent library (CDL) restraints added in 5.9 seconds 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8640 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 13 sheets defined 73.7% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'B' and resid 2633 through 2643 removed outlier: 3.636A pdb=" N ILE B2639 " --> pdb=" O GLN B2635 " (cutoff:3.500A) Processing helix chain 'B' and resid 2651 through 2668 removed outlier: 4.025A pdb=" N ASN B2668 " --> pdb=" O GLU B2664 " (cutoff:3.500A) Processing helix chain 'B' and resid 2676 through 2680 Processing helix chain 'B' and resid 2688 through 2696 removed outlier: 4.190A pdb=" N LEU B2692 " --> pdb=" O THR B2688 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B2693 " --> pdb=" O ASN B2689 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B2694 " --> pdb=" O ILE B2690 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B2696 " --> pdb=" O LEU B2692 " (cutoff:3.500A) Processing helix chain 'B' and resid 2701 through 2713 removed outlier: 3.702A pdb=" N VAL B2712 " --> pdb=" O GLU B2708 " (cutoff:3.500A) Processing helix chain 'B' and resid 2724 through 2740 Processing helix chain 'B' and resid 2744 through 2746 No H-bonds generated for 'chain 'B' and resid 2744 through 2746' Processing helix chain 'B' and resid 2747 through 2753 removed outlier: 3.721A pdb=" N LYS B2751 " --> pdb=" O THR B2747 " (cutoff:3.500A) Processing helix chain 'B' and resid 2758 through 2764 removed outlier: 3.681A pdb=" N CYS B2762 " --> pdb=" O LEU B2758 " (cutoff:3.500A) Processing helix chain 'B' and resid 2774 through 2785 removed outlier: 3.705A pdb=" N SER B2779 " --> pdb=" O ALA B2775 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B2780 " --> pdb=" O LEU B2776 " (cutoff:3.500A) Processing helix chain 'B' and resid 2788 through 2807 removed outlier: 4.267A pdb=" N MET B2793 " --> pdb=" O PRO B2789 " (cutoff:3.500A) Processing helix chain 'B' and resid 2810 through 2828 removed outlier: 3.724A pdb=" N GLN B2822 " --> pdb=" O ASP B2818 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B2823 " --> pdb=" O GLU B2819 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B2824 " --> pdb=" O GLY B2820 " (cutoff:3.500A) Processing helix chain 'B' and resid 2835 through 2866 removed outlier: 4.040A pdb=" N LEU B2842 " --> pdb=" O ALA B2838 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B2845 " --> pdb=" O TRP B2841 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B2846 " --> pdb=" O LEU B2842 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N TYR B2849 " --> pdb=" O GLY B2845 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B2851 " --> pdb=" O GLN B2847 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B2855 " --> pdb=" O GLU B2851 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B2856 " --> pdb=" O PHE B2852 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B2857 " --> pdb=" O LEU B2853 " (cutoff:3.500A) Processing helix chain 'B' and resid 2875 through 2886 Processing helix chain 'B' and resid 2895 through 2901 removed outlier: 4.574A pdb=" N ASN B2899 " --> pdb=" O VAL B2895 " (cutoff:3.500A) Processing helix chain 'B' and resid 2902 through 2917 removed outlier: 3.656A pdb=" N GLN B2906 " --> pdb=" O VAL B2902 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B2908 " --> pdb=" O TRP B2904 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B2911 " --> pdb=" O HIS B2907 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B2915 " --> pdb=" O VAL B2911 " (cutoff:3.500A) Processing helix chain 'B' and resid 2918 through 2923 Proline residue: B2921 - end of helix No H-bonds generated for 'chain 'B' and resid 2918 through 2923' Processing helix chain 'B' and resid 2942 through 2957 removed outlier: 3.556A pdb=" N VAL B2946 " --> pdb=" O GLU B2942 " (cutoff:3.500A) Processing helix chain 'B' and resid 2961 through 2970 removed outlier: 4.318A pdb=" N SER B2965 " --> pdb=" O ASP B2961 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B2967 " --> pdb=" O CYS B2963 " (cutoff:3.500A) Processing helix chain 'B' and resid 2981 through 2995 Processing helix chain 'B' and resid 2998 through 3008 Processing helix chain 'B' and resid 3016 through 3033 Processing helix chain 'B' and resid 3039 through 3050 Processing helix chain 'B' and resid 3054 through 3070 removed outlier: 3.803A pdb=" N ALA B3058 " --> pdb=" O ALA B3054 " (cutoff:3.500A) Processing helix chain 'B' and resid 3077 through 3093 removed outlier: 3.847A pdb=" N SER B3083 " --> pdb=" O SER B3079 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B3084 " --> pdb=" O ASN B3080 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY B3090 " --> pdb=" O LEU B3086 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU B3091 " --> pdb=" O GLN B3087 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B3092 " --> pdb=" O ALA B3088 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS B3093 " --> pdb=" O ALA B3089 " (cutoff:3.500A) Processing helix chain 'B' and resid 3094 through 3098 removed outlier: 3.855A pdb=" N ARG B3098 " --> pdb=" O SER B3095 " (cutoff:3.500A) Processing helix chain 'B' and resid 3099 through 3111 removed outlier: 3.577A pdb=" N ARG B3103 " --> pdb=" O GLU B3099 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B3104 " --> pdb=" O LEU B3100 " (cutoff:3.500A) Processing helix chain 'B' and resid 3116 through 3122 removed outlier: 3.592A pdb=" N ALA B3120 " --> pdb=" O MET B3116 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B3122 " --> pdb=" O THR B3118 " (cutoff:3.500A) Processing helix chain 'B' and resid 3129 through 3133 removed outlier: 3.581A pdb=" N TRP B3133 " --> pdb=" O VAL B3130 " (cutoff:3.500A) Processing helix chain 'B' and resid 3138 through 3142 Processing helix chain 'B' and resid 3149 through 3163 Processing helix chain 'B' and resid 3166 through 3181 removed outlier: 4.157A pdb=" N GLN B3170 " --> pdb=" O ALA B3166 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B3173 " --> pdb=" O PHE B3169 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR B3174 " --> pdb=" O GLN B3170 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) Processing helix chain 'B' and resid 3204 through 3217 Processing helix chain 'B' and resid 3222 through 3237 removed outlier: 4.054A pdb=" N LEU B3226 " --> pdb=" O LEU B3222 " (cutoff:3.500A) Processing helix chain 'B' and resid 3242 through 3263 Processing helix chain 'B' and resid 3274 through 3285 Processing helix chain 'B' and resid 3292 through 3300 Processing helix chain 'B' and resid 3308 through 3327 Processing helix chain 'B' and resid 3356 through 3360 removed outlier: 4.208A pdb=" N LEU B3360 " --> pdb=" O GLN B3357 " (cutoff:3.500A) Processing helix chain 'B' and resid 3410 through 3432 removed outlier: 3.842A pdb=" N ARG B3414 " --> pdb=" O VAL B3410 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU B3417 " --> pdb=" O SER B3413 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B3421 " --> pdb=" O GLU B3417 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B3422 " --> pdb=" O ARG B3418 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B3423 " --> pdb=" O MET B3419 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS B3432 " --> pdb=" O LYS B3428 " (cutoff:3.500A) Processing helix chain 'B' and resid 3436 through 3440 Processing helix chain 'B' and resid 3467 through 3479 removed outlier: 3.741A pdb=" N ASN B3472 " --> pdb=" O HIS B3468 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B3473 " --> pdb=" O GLU B3469 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS B3475 " --> pdb=" O HIS B3471 " (cutoff:3.500A) Processing helix chain 'B' and resid 3482 through 3498 removed outlier: 3.897A pdb=" N GLN B3486 " --> pdb=" O PRO B3482 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B3496 " --> pdb=" O LYS B3492 " (cutoff:3.500A) Processing helix chain 'B' and resid 3504 through 3522 removed outlier: 3.937A pdb=" N THR B3519 " --> pdb=" O ASN B3515 " (cutoff:3.500A) Processing helix chain 'B' and resid 3526 through 3535 removed outlier: 4.583A pdb=" N THR B3532 " --> pdb=" O LYS B3528 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B3533 " --> pdb=" O ASP B3529 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B3534 " --> pdb=" O HIS B3530 " (cutoff:3.500A) Processing helix chain 'B' and resid 3540 through 3553 removed outlier: 4.195A pdb=" N PHE B3544 " --> pdb=" O ASP B3540 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG B3545 " --> pdb=" O PHE B3541 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B3546 " --> pdb=" O TRP B3542 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B3547 " --> pdb=" O LEU B3543 " (cutoff:3.500A) Processing helix chain 'B' and resid 3555 through 3561 Processing helix chain 'B' and resid 3637 through 3654 removed outlier: 4.012A pdb=" N PHE B3641 " --> pdb=" O LEU B3637 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B3642 " --> pdb=" O GLU B3638 " (cutoff:3.500A) Processing helix chain 'B' and resid 3658 through 3680 removed outlier: 3.579A pdb=" N LEU B3665 " --> pdb=" O THR B3661 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE B3666 " --> pdb=" O TYR B3662 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP B3669 " --> pdb=" O LEU B3665 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B3671 " --> pdb=" O ILE B3667 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER B3673 " --> pdb=" O ASP B3669 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B3679 " --> pdb=" O PHE B3675 " (cutoff:3.500A) Processing helix chain 'B' and resid 3688 through 3704 Processing helix chain 'B' and resid 3718 through 3729 Processing helix chain 'B' and resid 3729 through 3735 removed outlier: 3.663A pdb=" N ARG B3735 " --> pdb=" O ARG B3731 " (cutoff:3.500A) Processing helix chain 'B' and resid 3740 through 3744 removed outlier: 4.503A pdb=" N TRP B3743 " --> pdb=" O PHE B3740 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE B3744 " --> pdb=" O MET B3741 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3740 through 3744' Processing helix chain 'C' and resid 649 through 662 removed outlier: 3.873A pdb=" N ASP C 654 " --> pdb=" O TRP C 650 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 660 " --> pdb=" O GLN C 656 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 674 removed outlier: 3.692A pdb=" N LEU C 671 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 672 " --> pdb=" O ASN C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 688 removed outlier: 3.888A pdb=" N SER C 683 " --> pdb=" O ARG C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 706 removed outlier: 3.729A pdb=" N PHE C 700 " --> pdb=" O CYS C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 removed outlier: 4.172A pdb=" N LYS C 713 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 731 removed outlier: 5.373A pdb=" N ALA C 727 " --> pdb=" O TRP C 723 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS C 728 " --> pdb=" O LEU C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 769 removed outlier: 3.723A pdb=" N ARG C 754 " --> pdb=" O ARG C 750 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 756 " --> pdb=" O HIS C 752 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C 759 " --> pdb=" O LEU C 755 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE C 761 " --> pdb=" O TRP C 757 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE C 764 " --> pdb=" O MET C 760 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS C 766 " --> pdb=" O GLU C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 809 removed outlier: 3.782A pdb=" N GLN C 805 " --> pdb=" O LEU C 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 9 Processing helix chain 'D' and resid 53 through 62 Processing helix chain 'D' and resid 150 through 164 removed outlier: 3.562A pdb=" N UNK D 154 " --> pdb=" O UNK D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 170 through 181 removed outlier: 4.520A pdb=" N UNK D 177 " --> pdb=" O UNK D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 283 Processing helix chain 'D' and resid 284 through 291 Processing helix chain 'D' and resid 310 through 319 removed outlier: 3.802A pdb=" N UNK D 317 " --> pdb=" O UNK D 313 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N UNK D 319 " --> pdb=" O UNK D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 367 Processing helix chain 'D' and resid 418 through 431 removed outlier: 3.823A pdb=" N UNK D 422 " --> pdb=" O UNK D 418 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N UNK D 425 " --> pdb=" O UNK D 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK D 426 " --> pdb=" O UNK D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 448 Processing helix chain 'H' and resid 4 through 16 Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 46 through 62 removed outlier: 3.889A pdb=" N ILE H 56 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN H 57 " --> pdb=" O ASN H 53 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 86 removed outlier: 3.999A pdb=" N THR H 82 " --> pdb=" O ASN H 78 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE H 83 " --> pdb=" O ASP H 79 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'H' and resid 109 through 124 Processing helix chain 'H' and resid 182 through 195 removed outlier: 4.194A pdb=" N LYS H 186 " --> pdb=" O GLU H 182 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 243 Proline residue: H 229 - end of helix removed outlier: 3.654A pdb=" N ILE H 243 " --> pdb=" O LEU H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 269 Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.608A pdb=" N GLN A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 11 " --> pdb=" O ILE A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 36 removed outlier: 4.163A pdb=" N LEU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 112 through 130 removed outlier: 4.017A pdb=" N SER A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 159 removed outlier: 3.825A pdb=" N ILE A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 150 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.860A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 242 " --> pdb=" O TYR A 238 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 288 through 303 Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 323 through 336 removed outlier: 3.654A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 361 removed outlier: 4.032A pdb=" N LEU A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.899A pdb=" N ASP A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 405 removed outlier: 3.581A pdb=" N TYR A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 425 Processing helix chain 'A' and resid 431 through 451 Processing helix chain 'A' and resid 459 through 503 removed outlier: 4.045A pdb=" N LEU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE A 485 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR A 488 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 494 " --> pdb=" O GLY A 490 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 499 " --> pdb=" O HIS A 495 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 503 " --> pdb=" O LYS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.532A pdb=" N LYS A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 Processing helix chain 'A' and resid 582 through 605 Processing helix chain 'A' and resid 630 through 647 Processing helix chain 'A' and resid 675 through 692 Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 704 through 713 Processing helix chain 'A' and resid 719 through 731 removed outlier: 3.739A pdb=" N LEU A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 748 removed outlier: 3.838A pdb=" N LEU A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 746 " --> pdb=" O ARG A 742 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A 747 " --> pdb=" O PHE A 743 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 748 " --> pdb=" O LEU A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 776 removed outlier: 3.580A pdb=" N PHE A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN A 774 " --> pdb=" O PHE A 770 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 775 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 798 removed outlier: 4.227A pdb=" N LEU A 796 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 798 " --> pdb=" O ASN A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Processing helix chain 'A' and resid 813 through 818 Processing helix chain 'A' and resid 830 through 845 removed outlier: 4.008A pdb=" N GLN A 836 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 863 removed outlier: 3.647A pdb=" N GLU A 856 " --> pdb=" O PRO A 852 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 857 " --> pdb=" O HIS A 853 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS A 862 " --> pdb=" O TYR A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 removed outlier: 3.502A pdb=" N PHE A 878 " --> pdb=" O PRO A 874 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 879 " --> pdb=" O TYR A 875 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 874 through 879' Processing helix chain 'A' and resid 879 through 886 removed outlier: 3.659A pdb=" N LEU A 883 " --> pdb=" O LEU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 904 removed outlier: 3.956A pdb=" N GLY A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 913 through 930 Proline residue: A 919 - end of helix removed outlier: 5.339A pdb=" N LYS A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA A 927 " --> pdb=" O ASP A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 952 removed outlier: 4.181A pdb=" N LEU A 952 " --> pdb=" O ILE A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 969 through 973 Processing helix chain 'A' and resid 997 through 1006 Processing helix chain 'A' and resid 1011 through 1029 removed outlier: 4.093A pdb=" N ALA A1017 " --> pdb=" O TYR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1051 removed outlier: 3.538A pdb=" N VAL A1047 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A1048 " --> pdb=" O LYS A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1091 removed outlier: 3.801A pdb=" N PHE A1087 " --> pdb=" O LEU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1126 removed outlier: 3.895A pdb=" N LEU A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP A1108 " --> pdb=" O ASN A1104 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A1113 " --> pdb=" O HIS A1109 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN A1114 " --> pdb=" O PHE A1110 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A1115 " --> pdb=" O CYS A1111 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN A1124 " --> pdb=" O LEU A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1153 Proline residue: A1150 - end of helix Processing helix chain 'A' and resid 1158 through 1174 Processing helix chain 'A' and resid 1183 through 1202 Proline residue: A1191 - end of helix Processing helix chain 'A' and resid 1207 through 1224 removed outlier: 3.861A pdb=" N LYS A1224 " --> pdb=" O ILE A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1247 removed outlier: 3.510A pdb=" N TYR A1233 " --> pdb=" O PHE A1229 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN A1239 " --> pdb=" O TYR A1235 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY A1240 " --> pdb=" O ASN A1236 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1271 removed outlier: 3.828A pdb=" N SER A1269 " --> pdb=" O ILE A1265 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A1270 " --> pdb=" O ASP A1266 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1293 Processing helix chain 'A' and resid 1299 through 1315 removed outlier: 3.617A pdb=" N VAL A1303 " --> pdb=" O ALA A1299 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN A1305 " --> pdb=" O PRO A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1332 removed outlier: 3.559A pdb=" N LYS A1324 " --> pdb=" O ILE A1320 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1359 Processing helix chain 'A' and resid 1372 through 1385 Processing helix chain 'A' and resid 1402 through 1419 removed outlier: 3.573A pdb=" N GLU A1406 " --> pdb=" O TYR A1402 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A1414 " --> pdb=" O GLN A1410 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS A1415 " --> pdb=" O LEU A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1447 Processing helix chain 'A' and resid 1453 through 1469 Processing helix chain 'A' and resid 1475 through 1488 Proline residue: A1484 - end of helix Processing helix chain 'A' and resid 1497 through 1507 Processing helix chain 'A' and resid 1520 through 1529 Processing helix chain 'A' and resid 1535 through 1543 Processing helix chain 'A' and resid 1547 through 1562 removed outlier: 3.755A pdb=" N ILE A1555 " --> pdb=" O ILE A1551 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A1559 " --> pdb=" O ILE A1555 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N HIS A1560 " --> pdb=" O ILE A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1582 Processing helix chain 'A' and resid 1592 through 1600 removed outlier: 3.854A pdb=" N ALA A1597 " --> pdb=" O ARG A1593 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A1598 " --> pdb=" O THR A1594 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A1599 " --> pdb=" O PRO A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1615 Processing helix chain 'A' and resid 1617 through 1630 removed outlier: 4.191A pdb=" N PHE A1623 " --> pdb=" O GLN A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1653 removed outlier: 4.227A pdb=" N TYR A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A1649 " --> pdb=" O ASP A1645 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A1652 " --> pdb=" O TYR A1648 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1680 Processing helix chain 'A' and resid 1692 through 1707 Processing helix chain 'A' and resid 1717 through 1735 Processing helix chain 'A' and resid 1741 through 1750 removed outlier: 3.795A pdb=" N LEU A1745 " --> pdb=" O ASN A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1760 through 1768 Processing helix chain 'A' and resid 1777 through 1788 Processing helix chain 'A' and resid 1799 through 1816 Processing helix chain 'A' and resid 1830 through 1844 Processing helix chain 'A' and resid 1860 through 1872 removed outlier: 3.521A pdb=" N LEU A1864 " --> pdb=" O PHE A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1880 through 1895 Processing helix chain 'A' and resid 1900 through 1910 removed outlier: 3.526A pdb=" N TYR A1906 " --> pdb=" O LYS A1902 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A1907 " --> pdb=" O GLN A1903 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A1908 " --> pdb=" O SER A1904 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A1909 " --> pdb=" O ALA A1905 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A1910 " --> pdb=" O TYR A1906 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1919 No H-bonds generated for 'chain 'A' and resid 1917 through 1919' Processing helix chain 'A' and resid 1920 through 1931 Processing helix chain 'A' and resid 1938 through 1953 Proline residue: A1951 - end of helix Processing helix chain 'A' and resid 1961 through 1973 Processing helix chain 'A' and resid 1980 through 1990 removed outlier: 3.806A pdb=" N TYR A1986 " --> pdb=" O ASN A1982 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A1988 " --> pdb=" O ILE A1984 " (cutoff:3.500A) Processing helix chain 'A' and resid 2000 through 2017 Processing helix chain 'A' and resid 2024 through 2043 Processing helix chain 'A' and resid 2091 through 2107 Processing helix chain 'A' and resid 2116 through 2130 Processing helix chain 'A' and resid 2141 through 2147 Processing helix chain 'A' and resid 2156 through 2173 Processing helix chain 'A' and resid 2178 through 2192 Proline residue: A2185 - end of helix removed outlier: 3.577A pdb=" N GLU A2192 " --> pdb=" O GLN A2188 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2219 Processing helix chain 'A' and resid 2226 through 2244 Proline residue: A2231 - end of helix Processing helix chain 'A' and resid 2252 through 2267 Processing helix chain 'A' and resid 2271 through 2289 Proline residue: A2277 - end of helix Processing helix chain 'A' and resid 2302 through 2318 Processing helix chain 'A' and resid 2328 through 2338 Processing helix chain 'A' and resid 2345 through 2359 removed outlier: 3.912A pdb=" N LEU A2349 " --> pdb=" O ASP A2345 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A2357 " --> pdb=" O VAL A2353 " (cutoff:3.500A) Processing helix chain 'A' and resid 2369 through 2384 Processing helix chain 'A' and resid 2387 through 2401 removed outlier: 3.503A pdb=" N LYS A2392 " --> pdb=" O PRO A2388 " (cutoff:3.500A) Processing helix chain 'A' and resid 2409 through 2418 removed outlier: 3.886A pdb=" N ARG A2415 " --> pdb=" O GLU A2411 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A2417 " --> pdb=" O THR A2413 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A2418 " --> pdb=" O VAL A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2431 through 2442 Processing helix chain 'A' and resid 2451 through 2461 Processing helix chain 'A' and resid 2468 through 2480 Processing helix chain 'A' and resid 2518 through 2531 removed outlier: 3.552A pdb=" N HIS A2526 " --> pdb=" O PHE A2522 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A2527 " --> pdb=" O VAL A2523 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A2531 " --> pdb=" O ILE A2527 " (cutoff:3.500A) Processing helix chain 'A' and resid 2539 through 2550 removed outlier: 4.279A pdb=" N ILE A2546 " --> pdb=" O ILE A2542 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A2547 " --> pdb=" O ASP A2543 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A2550 " --> pdb=" O ILE A2546 " (cutoff:3.500A) Processing helix chain 'A' and resid 2552 through 2568 removed outlier: 3.958A pdb=" N ILE A2556 " --> pdb=" O ASP A2552 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS A2557 " --> pdb=" O PRO A2553 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A2558 " --> pdb=" O LYS A2554 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL A2561 " --> pdb=" O HIS A2557 " (cutoff:3.500A) Proline residue: A2565 - end of helix Processing helix chain 'A' and resid 2573 through 2587 Processing helix chain 'A' and resid 2599 through 2610 removed outlier: 4.765A pdb=" N LEU A2606 " --> pdb=" O VAL A2602 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A2608 " --> pdb=" O ASN A2604 " (cutoff:3.500A) Processing helix chain 'A' and resid 2619 through 2626 Processing helix chain 'F' and resid 82 through 97 removed outlier: 3.531A pdb=" N GLN F 95 " --> pdb=" O GLN F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 removed outlier: 3.589A pdb=" N LEU F 125 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 147 Processing helix chain 'F' and resid 176 through 180 Processing helix chain 'F' and resid 186 through 198 Processing helix chain 'F' and resid 226 through 235 removed outlier: 3.912A pdb=" N TYR F 230 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 243 removed outlier: 3.591A pdb=" N LYS F 243 " --> pdb=" O PHE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 264 removed outlier: 4.643A pdb=" N LYS F 259 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR F 260 " --> pdb=" O GLU F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 294 removed outlier: 4.482A pdb=" N ALA F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 300 Processing helix chain 'F' and resid 384 through 396 Processing helix chain 'F' and resid 400 through 406 Processing helix chain 'F' and resid 419 through 432 removed outlier: 3.596A pdb=" N ILE F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 461 removed outlier: 3.925A pdb=" N TYR F 450 " --> pdb=" O ILE F 446 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N SER F 452 " --> pdb=" O ARG F 448 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP F 453 " --> pdb=" O GLN F 449 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY F 456 " --> pdb=" O SER F 452 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 469 Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 482 through 487 removed outlier: 3.655A pdb=" N ARG F 487 " --> pdb=" O LEU F 484 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.728A pdb=" N MET G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR G 89 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE G 90 " --> pdb=" O TRP G 86 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR G 91 " --> pdb=" O HIS G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 112 through 127 removed outlier: 3.539A pdb=" N PHE G 124 " --> pdb=" O THR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 181 through 195 removed outlier: 3.561A pdb=" N LEU G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 217 Processing helix chain 'G' and resid 222 through 232 removed outlier: 3.783A pdb=" N THR G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA G 231 " --> pdb=" O MET G 227 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 257 removed outlier: 4.206A pdb=" N ALA G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 261 removed outlier: 3.782A pdb=" N LEU G 261 " --> pdb=" O PRO G 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 258 through 261' Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 283 Processing helix chain 'G' and resid 289 through 296 Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 319 removed outlier: 4.083A pdb=" N ARG G 312 " --> pdb=" O GLY G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 352 through 356 Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 366 through 372 Processing helix chain 'E' and resid 358 through 366 removed outlier: 3.780A pdb=" N LEU E 362 " --> pdb=" O HIS E 358 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 363 " --> pdb=" O GLN E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 396 removed outlier: 3.574A pdb=" N ALA E 371 " --> pdb=" O LYS E 367 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP E 372 " --> pdb=" O TRP E 368 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS E 378 " --> pdb=" O LYS E 374 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP E 395 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 396 " --> pdb=" O LYS E 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3465 through 3466 removed outlier: 3.989A pdb=" N THR B3465 " --> pdb=" O VAL B3574 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B3574 " --> pdb=" O THR B3465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 38 through 41 removed outlier: 3.626A pdb=" N TYR F 138 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS F 137 " --> pdb=" O VAL F 470 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL F 470 " --> pdb=" O CYS F 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 43 through 45 Processing sheet with id=AA4, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AA5, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.603A pdb=" N VAL F 409 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 209 through 211 Processing sheet with id=AA7, first strand: chain 'G' and resid 8 through 10 Processing sheet with id=AA8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'G' and resid 103 through 107 removed outlier: 3.660A pdb=" N TYR G 133 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER G 135 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU G 107 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.868A pdb=" N VAL G 162 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G 176 " --> pdb=" O VAL G 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.564A pdb=" N VAL G 152 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE G 165 " --> pdb=" O GLY G 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 238 through 241 1849 hydrogen bonds defined for protein. 5379 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: 10.83 Time building geometry restraints manager: 11.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.52: 20943 1.52 - 1.88: 4893 1.88 - 2.24: 0 2.24 - 2.60: 0 2.60 - 2.96: 1 Bond restraints: 25837 Sorted by residual: bond pdb=" C ASP A1994 " pdb=" N ASN A1998 " ideal model delta sigma weight residual 1.332 2.957 -1.625 1.40e-02 5.10e+03 1.35e+04 bond pdb=" C GLU A 410 " pdb=" N ILE A 411 " ideal model delta sigma weight residual 1.332 1.555 -0.223 1.36e-02 5.41e+03 2.68e+02 bond pdb=" C TYR F 475 " pdb=" O TYR F 475 " ideal model delta sigma weight residual 1.236 1.166 0.070 1.16e-02 7.43e+03 3.60e+01 bond pdb=" CA GLU F 447 " pdb=" C GLU F 447 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.39e-02 5.18e+03 1.70e+01 bond pdb=" CA HIS B3497 " pdb=" C HIS B3497 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.29e-02 6.01e+03 1.68e+01 ... (remaining 25832 not shown) Histogram of bond angle deviations from ideal: 88.00 - 97.31: 1 97.31 - 106.61: 440 106.61 - 115.91: 16197 115.91 - 125.21: 18648 125.21 - 134.52: 250 Bond angle restraints: 35536 Sorted by residual: angle pdb=" O ASP A1994 " pdb=" C ASP A1994 " pdb=" N ASN A1998 " ideal model delta sigma weight residual 122.59 88.00 34.59 1.33e+00 5.65e-01 6.76e+02 angle pdb=" N PRO A1919 " pdb=" CA PRO A1919 " pdb=" CB PRO A1919 " ideal model delta sigma weight residual 102.81 110.93 -8.12 6.70e-01 2.23e+00 1.47e+02 angle pdb=" C GLY C 714 " pdb=" N PRO C 715 " pdb=" CA PRO C 715 " ideal model delta sigma weight residual 119.84 134.52 -14.68 1.25e+00 6.40e-01 1.38e+02 angle pdb=" C GLU B3618 " pdb=" N PRO B3619 " pdb=" CA PRO B3619 " ideal model delta sigma weight residual 119.84 105.29 14.55 1.25e+00 6.40e-01 1.35e+02 angle pdb=" N HIS B3497 " pdb=" CA HIS B3497 " pdb=" C HIS B3497 " ideal model delta sigma weight residual 111.36 98.69 12.67 1.09e+00 8.42e-01 1.35e+02 ... (remaining 35531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 14760 16.91 - 33.81: 360 33.81 - 50.72: 149 50.72 - 67.63: 59 67.63 - 84.53: 8 Dihedral angle restraints: 15336 sinusoidal: 2316 harmonic: 13020 Sorted by residual: dihedral pdb=" C VAL B3152 " pdb=" N VAL B3152 " pdb=" CA VAL B3152 " pdb=" CB VAL B3152 " ideal model delta harmonic sigma weight residual -122.00 -137.59 15.59 0 2.50e+00 1.60e-01 3.89e+01 dihedral pdb=" CA UNK D 200 " pdb=" C UNK D 200 " pdb=" N UNK D 201 " pdb=" CA UNK D 201 " ideal model delta harmonic sigma weight residual -180.00 -150.01 -29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA PRO F 433 " pdb=" C PRO F 433 " pdb=" N SER F 434 " pdb=" CA SER F 434 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 15333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4241 0.100 - 0.201: 329 0.201 - 0.301: 79 0.301 - 0.401: 6 0.401 - 0.501: 2 Chirality restraints: 4657 Sorted by residual: chirality pdb=" CA VAL B3152 " pdb=" N VAL B3152 " pdb=" C VAL B3152 " pdb=" CB VAL B3152 " both_signs ideal model delta sigma weight residual False 2.44 1.94 0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" CA GLU F 70 " pdb=" N GLU F 70 " pdb=" C GLU F 70 " pdb=" CB GLU F 70 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA LYS B3348 " pdb=" N LYS B3348 " pdb=" C LYS B3348 " pdb=" CB LYS B3348 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 4654 not shown) Planarity restraints: 4839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A1994 " 0.163 2.00e-02 2.50e+03 2.30e-01 5.30e+02 pdb=" C ASP A1994 " -0.388 2.00e-02 2.50e+03 pdb=" O ASP A1994 " 0.180 2.00e-02 2.50e+03 pdb=" N ASN A1998 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B3452 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO B3453 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO B3453 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO B3453 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B3618 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B3619 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO B3619 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B3619 " -0.065 5.00e-02 4.00e+02 ... (remaining 4836 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 131 2.25 - 2.91: 14374 2.91 - 3.57: 40512 3.57 - 4.24: 51583 4.24 - 4.90: 83414 Nonbonded interactions: 190014 Sorted by model distance: nonbonded pdb=" CA UNK D 418 " pdb=" CG2 THR F 441 " model vdw 1.581 3.890 nonbonded pdb=" O HIS F 444 " pdb=" N ILE F 446 " model vdw 1.700 2.520 nonbonded pdb=" O LYS A1093 " pdb=" N LEU A1095 " model vdw 1.706 2.520 nonbonded pdb=" O THR A 430 " pdb=" N GLN A 432 " model vdw 1.730 2.520 nonbonded pdb=" O GLN C 721 " pdb=" CB LEU C 724 " model vdw 1.746 3.440 ... (remaining 190009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 6.890 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 72.650 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.012 1.625 25837 Z= 0.969 Angle : 1.244 34.587 35536 Z= 0.868 Chirality : 0.062 0.501 4657 Planarity : 0.006 0.230 4839 Dihedral : 11.531 84.533 6696 Min Nonbonded Distance : 1.581 Molprobity Statistics. All-atom Clashscore : 41.26 Ramachandran Plot: Outliers : 5.33 % Allowed : 15.47 % Favored : 79.20 % Rotamer: Outliers : 14.19 % Allowed : 6.27 % Favored : 79.54 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.73 (0.10), residues: 3866 helix: -3.31 (0.07), residues: 2422 sheet: -2.96 (0.47), residues: 98 loop : -4.58 (0.14), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 355 time to evaluate : 2.978 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 69 residues processed: 460 average time/residue: 0.3946 time to fit residues: 287.9833 Evaluate side-chains 304 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 235 time to evaluate : 3.044 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 69 outliers final: 1 residues processed: 69 average time/residue: 0.3444 time to fit residues: 44.7278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 4.9990 chunk 336 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 348 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 211 optimal weight: 0.5980 chunk 259 optimal weight: 10.0000 chunk 403 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3064 ASN B3367 HIS B3472 ASN B3732 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN F 154 ASN ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN G 73 HIS G 280 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 25837 Z= 0.296 Angle : 0.773 11.072 35536 Z= 0.421 Chirality : 0.043 0.256 4657 Planarity : 0.006 0.230 4839 Dihedral : 5.817 36.896 4436 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 1.68 % Allowed : 11.77 % Favored : 86.55 % Rotamer: Outliers : 0.58 % Allowed : 5.02 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.13), residues: 3868 helix: -0.40 (0.10), residues: 2598 sheet: -2.58 (0.48), residues: 106 loop : -4.00 (0.16), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 314 time to evaluate : 3.878 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: symmetry clash outliers start: 5 outliers final: 1 residues processed: 318 average time/residue: 0.3472 time to fit residues: 182.4052 Evaluate side-chains 231 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 2.773 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2337 time to fit residues: 4.0366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 0.1980 chunk 125 optimal weight: 10.0000 chunk 335 optimal weight: 5.9990 chunk 274 optimal weight: 0.0270 chunk 111 optimal weight: 1.9990 chunk 403 optimal weight: 5.9990 chunk 436 optimal weight: 7.9990 chunk 359 optimal weight: 7.9990 chunk 400 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 chunk 324 optimal weight: 10.0000 overall best weight: 2.8444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3064 ASN F 91 GLN F 96 ASN F 154 ASN ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25837 Z= 0.216 Angle : 0.645 7.742 35536 Z= 0.345 Chirality : 0.040 0.260 4657 Planarity : 0.004 0.113 4839 Dihedral : 5.046 33.307 4436 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 1.32 % Allowed : 10.19 % Favored : 88.49 % Rotamer: Outliers : 0.29 % Allowed : 3.76 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.24 (0.15), residues: 3868 helix: 1.24 (0.11), residues: 2639 sheet: -2.00 (0.51), residues: 96 loop : -3.53 (0.18), residues: 1133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 304 time to evaluate : 2.940 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: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 304 average time/residue: 0.3590 time to fit residues: 184.0211 Evaluate side-chains 225 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 2.921 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2512 time to fit residues: 4.5129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 6.9990 chunk 303 optimal weight: 10.0000 chunk 209 optimal weight: 0.0770 chunk 44 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 405 optimal weight: 30.0000 chunk 429 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 384 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3064 ASN B3444 ASN B3551 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN G 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25837 Z= 0.185 Angle : 0.598 9.746 35536 Z= 0.318 Chirality : 0.039 0.218 4657 Planarity : 0.004 0.111 4839 Dihedral : 4.751 34.022 4436 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 1.27 % Allowed : 9.00 % Favored : 89.73 % Rotamer: Outliers : 0.19 % Allowed : 2.61 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.47 (0.15), residues: 3868 helix: 1.78 (0.11), residues: 2630 sheet: -1.67 (0.50), residues: 101 loop : -3.24 (0.18), residues: 1137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 295 time to evaluate : 3.084 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 296 average time/residue: 0.3436 time to fit residues: 171.2065 Evaluate side-chains 230 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 3.254 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2673 time to fit residues: 4.6745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 7.9990 chunk 243 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 319 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 chunk 366 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 385 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B3660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN F 154 ASN ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN ** G 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 25837 Z= 0.296 Angle : 0.677 8.567 35536 Z= 0.367 Chirality : 0.042 0.236 4657 Planarity : 0.004 0.111 4839 Dihedral : 5.161 32.130 4436 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 1.22 % Allowed : 11.20 % Favored : 87.59 % Rotamer: Outliers : 0.19 % Allowed : 3.19 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.16 (0.14), residues: 3868 helix: 1.26 (0.10), residues: 2620 sheet: -2.50 (0.44), residues: 120 loop : -3.26 (0.18), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 3.005 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 outliers start: 1 outliers final: 1 residues processed: 284 average time/residue: 0.3498 time to fit residues: 166.5853 Evaluate side-chains 224 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 2.951 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2505 time to fit residues: 4.2183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 10.0000 chunk 386 optimal weight: 1.9990 chunk 84 optimal weight: 40.0000 chunk 251 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 429 optimal weight: 5.9990 chunk 356 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2752 HIS ** B3421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3732 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN F 154 ASN ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 GLN E 358 HIS E 359 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 25837 Z= 0.226 Angle : 0.616 11.797 35536 Z= 0.328 Chirality : 0.040 0.223 4657 Planarity : 0.004 0.111 4839 Dihedral : 4.890 31.536 4436 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 1.22 % Allowed : 8.92 % Favored : 89.86 % Rotamer: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3868 helix: 1.59 (0.11), residues: 2620 sheet: -2.13 (0.44), residues: 119 loop : -3.10 (0.18), residues: 1129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 3.035 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 outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.3597 time to fit residues: 168.8140 Evaluate side-chains 213 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.992 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 313 optimal weight: 7.9990 chunk 243 optimal weight: 5.9990 chunk 361 optimal weight: 6.9990 chunk 239 optimal weight: 20.0000 chunk 427 optimal weight: 0.9990 chunk 267 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 197 optimal weight: 30.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B3421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN F 162 HIS ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 GLN E 358 HIS E 359 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25837 Z= 0.252 Angle : 0.636 9.123 35536 Z= 0.344 Chirality : 0.041 0.263 4657 Planarity : 0.004 0.111 4839 Dihedral : 4.940 27.925 4436 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 1.19 % Allowed : 11.15 % Favored : 87.66 % Rotamer: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.97 % 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: 0.15 (0.14), residues: 3868 helix: 1.45 (0.10), residues: 2633 sheet: -1.57 (0.46), residues: 112 loop : -3.16 (0.18), residues: 1123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.307 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 outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3493 time to fit residues: 158.8604 Evaluate side-chains 210 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 10.0000 chunk 170 optimal weight: 0.5980 chunk 255 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 chunk 82 optimal weight: 4.9990 chunk 272 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 211 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 336 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2638 ASN ** B2844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3064 ASN ** B3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN F 451 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 GLN E 359 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 25837 Z= 0.173 Angle : 0.568 7.862 35536 Z= 0.303 Chirality : 0.039 0.271 4657 Planarity : 0.004 0.111 4839 Dihedral : 4.557 28.078 4436 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 1.09 % Allowed : 7.99 % Favored : 90.92 % Rotamer: Outliers : 0.10 % Allowed : 1.35 % Favored : 98.55 % 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: 0.82 (0.15), residues: 3868 helix: 1.98 (0.11), residues: 2640 sheet: -1.68 (0.48), residues: 101 loop : -2.95 (0.19), residues: 1127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 3.599 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.3373 time to fit residues: 153.2298 Evaluate side-chains 217 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 8.9990 chunk 409 optimal weight: 30.0000 chunk 374 optimal weight: 0.9990 chunk 398 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 313 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 360 optimal weight: 6.9990 chunk 377 optimal weight: 1.9990 chunk 397 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2638 ASN ** B2844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN F 154 ASN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 GLN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25837 Z= 0.180 Angle : 0.558 8.155 35536 Z= 0.297 Chirality : 0.039 0.288 4657 Planarity : 0.004 0.112 4839 Dihedral : 4.408 26.855 4436 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 1.03 % Allowed : 9.13 % Favored : 89.84 % Rotamer: Outliers : 0.10 % Allowed : 1.45 % Favored : 98.46 % 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: 0.98 (0.15), residues: 3868 helix: 2.11 (0.11), residues: 2645 sheet: -1.62 (0.50), residues: 101 loop : -2.91 (0.19), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 3.021 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.3432 time to fit residues: 158.5773 Evaluate side-chains 214 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.885 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 8.9990 chunk 421 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 293 optimal weight: 9.9990 chunk 442 optimal weight: 5.9990 chunk 407 optimal weight: 6.9990 chunk 352 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 272 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B3421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 444 HIS F 451 GLN G 296 ASN G 354 GLN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25837 Z= 0.261 Angle : 0.642 10.352 35536 Z= 0.347 Chirality : 0.041 0.301 4657 Planarity : 0.004 0.110 4839 Dihedral : 4.851 26.726 4436 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 1.09 % Allowed : 10.76 % Favored : 88.16 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3868 helix: 1.64 (0.10), residues: 2652 sheet: -1.44 (0.49), residues: 110 loop : -2.93 (0.19), residues: 1106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 3.033 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.3266 time to fit residues: 145.7462 Evaluate side-chains 212 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.986 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 3.9990 chunk 375 optimal weight: 7.9990 chunk 107 optimal weight: 40.0000 chunk 324 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 352 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 362 optimal weight: 40.0000 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN F 449 GLN F 451 GLN G 354 GLN E 358 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.079840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.069211 restraints weight = 243004.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069980 restraints weight = 194203.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.070732 restraints weight = 142806.278| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25837 Z= 0.187 Angle : 0.571 8.644 35536 Z= 0.305 Chirality : 0.040 0.286 4657 Planarity : 0.004 0.111 4839 Dihedral : 4.541 27.519 4436 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 1.03 % Allowed : 9.31 % Favored : 89.66 % Rotamer: Outliers : 0.10 % Allowed : 0.68 % Favored : 99.23 % 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: 0.85 (0.15), residues: 3868 helix: 1.96 (0.11), residues: 2654 sheet: -1.53 (0.54), residues: 94 loop : -2.87 (0.19), residues: 1120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4610.29 seconds wall clock time: 83 minutes 54.80 seconds (5034.80 seconds total)