Starting phenix.real_space_refine on Thu Feb 5 05:51:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qx1_53433/02_2026/9qx1_53433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qx1_53433/02_2026/9qx1_53433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qx1_53433/02_2026/9qx1_53433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qx1_53433/02_2026/9qx1_53433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qx1_53433/02_2026/9qx1_53433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qx1_53433/02_2026/9qx1_53433.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 104 5.16 5 C 9446 2.51 5 N 2558 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14940 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5946 Classifications: {'peptide': 753} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1523 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 179} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 5946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5946 Classifications: {'peptide': 753} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1523 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 179} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1897 SG CYS A2683 87.454 51.707 51.457 1.00 61.47 S ATOM 1918 SG CYS A2686 88.402 55.391 51.257 1.00 68.13 S ATOM 3070 SG CYS A3010 86.070 53.992 48.681 1.00 56.21 S ATOM 3091 SG CYS A3013 89.707 52.901 48.643 1.00 59.20 S ATOM 9366 SG CYS B2683 62.175 95.368 51.461 1.00 64.60 S ATOM 9387 SG CYS B2686 61.222 91.688 51.264 1.00 70.52 S ATOM 10539 SG CYS B3010 63.552 93.084 48.679 1.00 65.09 S ATOM 10560 SG CYS B3013 59.921 94.185 48.646 1.00 63.34 S Time building chain proxies: 3.54, per 1000 atoms: 0.24 Number of scatterers: 14940 At special positions: 0 Unit cell: (150.892, 148.356, 91.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 104 16.00 O 2830 8.00 N 2558 7.00 C 9446 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 - 3.00 Amino acid : True - 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: 1.34 Conformation dependent library (CDL) restraints added in 662.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4301 " pdb="ZN ZN A4301 " - pdb=" SG CYS A3010 " pdb="ZN ZN A4301 " - pdb=" SG CYS A2686 " pdb="ZN ZN A4301 " - pdb=" SG CYS A3013 " pdb="ZN ZN A4301 " - pdb=" SG CYS A2683 " pdb=" ZN B4301 " pdb="ZN ZN B4301 " - pdb=" SG CYS B3010 " pdb="ZN ZN B4301 " - pdb=" SG CYS B2686 " pdb="ZN ZN B4301 " - pdb=" SG CYS B2683 " pdb="ZN ZN B4301 " - pdb=" SG CYS B3013 " Number of angles added : 12 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 6 sheets defined 73.2% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 2443 through 2471 removed outlier: 3.921A pdb=" N GLU A2471 " --> pdb=" O ASP A2467 " (cutoff:3.500A) Processing helix chain 'A' and resid 2474 through 2493 removed outlier: 3.922A pdb=" N LEU A2478 " --> pdb=" O GLY A2474 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A2480 " --> pdb=" O GLN A2476 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE A2481 " --> pdb=" O GLN A2477 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A2493 " --> pdb=" O THR A2489 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2506 Processing helix chain 'A' and resid 2506 through 2517 removed outlier: 3.680A pdb=" N LEU A2510 " --> pdb=" O HIS A2506 " (cutoff:3.500A) Processing helix chain 'A' and resid 2518 through 2535 removed outlier: 3.604A pdb=" N GLN A2524 " --> pdb=" O VAL A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2541 through 2553 Processing helix chain 'A' and resid 2556 through 2567 Processing helix chain 'A' and resid 2571 through 2589 Processing helix chain 'A' and resid 2590 through 2604 Processing helix chain 'A' and resid 2604 through 2609 removed outlier: 4.085A pdb=" N LEU A2608 " --> pdb=" O THR A2604 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A2609 " --> pdb=" O ILE A2605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2604 through 2609' Processing helix chain 'A' and resid 2616 through 2631 Proline residue: A2628 - end of helix Processing helix chain 'A' and resid 2632 through 2657 Processing helix chain 'A' and resid 2658 through 2669 removed outlier: 3.771A pdb=" N MET A2662 " --> pdb=" O GLY A2658 " (cutoff:3.500A) Processing helix chain 'A' and resid 2672 through 2676 removed outlier: 3.521A pdb=" N SER A2675 " --> pdb=" O GLY A2672 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A2676 " --> pdb=" O TRP A2673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2672 through 2676' Processing helix chain 'A' and resid 2876 through 2911 removed outlier: 3.520A pdb=" N ARG A2880 " --> pdb=" O CYS A2876 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A2892 " --> pdb=" O THR A2888 " (cutoff:3.500A) Processing helix chain 'A' and resid 2928 through 2938 Processing helix chain 'A' and resid 2950 through 2987 Processing helix chain 'A' and resid 3000 through 3005 removed outlier: 4.092A pdb=" N TYR A3004 " --> pdb=" O ASN A3000 " (cutoff:3.500A) Processing helix chain 'A' and resid 3006 through 3009 removed outlier: 3.821A pdb=" N SER A3009 " --> pdb=" O THR A3006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3006 through 3009' Processing helix chain 'A' and resid 3010 through 3029 Processing helix chain 'A' and resid 3031 through 3040 Processing helix chain 'A' and resid 3043 through 3055 Processing helix chain 'A' and resid 3058 through 3070 Processing helix chain 'A' and resid 3074 through 3087 Processing helix chain 'A' and resid 3091 through 3098 Processing helix chain 'A' and resid 3105 through 3121 removed outlier: 4.060A pdb=" N LYS A3109 " --> pdb=" O THR A3105 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A3121 " --> pdb=" O ALA A3117 " (cutoff:3.500A) Processing helix chain 'A' and resid 3122 through 3139 Processing helix chain 'A' and resid 3140 through 3143 removed outlier: 3.532A pdb=" N VAL A3143 " --> pdb=" O THR A3140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3140 through 3143' Processing helix chain 'A' and resid 3144 through 3149 Processing helix chain 'A' and resid 3155 through 3165 removed outlier: 4.037A pdb=" N ILE A3159 " --> pdb=" O PRO A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3168 through 3172 Processing helix chain 'A' and resid 3189 through 3191 No H-bonds generated for 'chain 'A' and resid 3189 through 3191' Processing helix chain 'A' and resid 3192 through 3198 Processing helix chain 'A' and resid 3202 through 3218 Processing helix chain 'A' and resid 3222 through 3234 Processing helix chain 'A' and resid 3235 through 3239 removed outlier: 3.780A pdb=" N SER A3238 " --> pdb=" O SER A3235 " (cutoff:3.500A) Processing helix chain 'A' and resid 3245 through 3257 Processing helix chain 'A' and resid 3259 through 3269 Processing helix chain 'A' and resid 3270 through 3285 removed outlier: 3.530A pdb=" N TYR A3274 " --> pdb=" O GLN A3270 " (cutoff:3.500A) Processing helix chain 'A' and resid 3286 through 3289 Processing helix chain 'A' and resid 3292 through 3315 Processing helix chain 'A' and resid 3317 through 3327 Processing helix chain 'A' and resid 3331 through 3344 Processing helix chain 'A' and resid 3350 through 3368 Processing helix chain 'A' and resid 3371 through 3383 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 325 through 333 Processing helix chain 'C' and resid 336 through 349 Processing helix chain 'C' and resid 399 through 403 Processing helix chain 'C' and resid 425 through 446 Processing helix chain 'C' and resid 459 through 469 Processing helix chain 'C' and resid 470 through 472 No H-bonds generated for 'chain 'C' and resid 470 through 472' Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'B' and resid 2444 through 2471 removed outlier: 3.868A pdb=" N GLU B2471 " --> pdb=" O ASP B2467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2474 through 2493 removed outlier: 3.890A pdb=" N LEU B2478 " --> pdb=" O GLY B2474 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B2479 " --> pdb=" O HIS B2475 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU B2480 " --> pdb=" O GLN B2476 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B2481 " --> pdb=" O GLN B2477 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B2493 " --> pdb=" O THR B2489 " (cutoff:3.500A) Processing helix chain 'B' and resid 2495 through 2506 Processing helix chain 'B' and resid 2506 through 2517 removed outlier: 3.711A pdb=" N LEU B2510 " --> pdb=" O HIS B2506 " (cutoff:3.500A) Processing helix chain 'B' and resid 2518 through 2535 removed outlier: 3.598A pdb=" N GLN B2524 " --> pdb=" O VAL B2520 " (cutoff:3.500A) Processing helix chain 'B' and resid 2541 through 2553 Processing helix chain 'B' and resid 2556 through 2567 Processing helix chain 'B' and resid 2571 through 2589 Processing helix chain 'B' and resid 2590 through 2604 Processing helix chain 'B' and resid 2604 through 2609 removed outlier: 4.079A pdb=" N LEU B2608 " --> pdb=" O THR B2604 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B2609 " --> pdb=" O ILE B2605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2604 through 2609' Processing helix chain 'B' and resid 2616 through 2631 Proline residue: B2628 - end of helix Processing helix chain 'B' and resid 2632 through 2657 Processing helix chain 'B' and resid 2658 through 2669 removed outlier: 3.760A pdb=" N MET B2662 " --> pdb=" O GLY B2658 " (cutoff:3.500A) Processing helix chain 'B' and resid 2672 through 2676 removed outlier: 3.879A pdb=" N ILE B2676 " --> pdb=" O TRP B2673 " (cutoff:3.500A) Processing helix chain 'B' and resid 2876 through 2911 removed outlier: 3.517A pdb=" N ARG B2880 " --> pdb=" O CYS B2876 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B2892 " --> pdb=" O THR B2888 " (cutoff:3.500A) Processing helix chain 'B' and resid 2928 through 2938 Processing helix chain 'B' and resid 2950 through 2987 Processing helix chain 'B' and resid 3000 through 3005 removed outlier: 4.126A pdb=" N TYR B3004 " --> pdb=" O ASN B3000 " (cutoff:3.500A) Processing helix chain 'B' and resid 3006 through 3009 removed outlier: 3.823A pdb=" N SER B3009 " --> pdb=" O THR B3006 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3006 through 3009' Processing helix chain 'B' and resid 3010 through 3029 Processing helix chain 'B' and resid 3031 through 3041 Processing helix chain 'B' and resid 3043 through 3055 Processing helix chain 'B' and resid 3058 through 3070 Processing helix chain 'B' and resid 3074 through 3087 Processing helix chain 'B' and resid 3091 through 3098 Processing helix chain 'B' and resid 3105 through 3121 removed outlier: 4.097A pdb=" N LYS B3109 " --> pdb=" O THR B3105 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B3121 " --> pdb=" O ALA B3117 " (cutoff:3.500A) Processing helix chain 'B' and resid 3122 through 3139 Processing helix chain 'B' and resid 3140 through 3143 removed outlier: 3.537A pdb=" N VAL B3143 " --> pdb=" O THR B3140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3140 through 3143' Processing helix chain 'B' and resid 3144 through 3149 Processing helix chain 'B' and resid 3155 through 3165 removed outlier: 4.049A pdb=" N ILE B3159 " --> pdb=" O PRO B3155 " (cutoff:3.500A) Processing helix chain 'B' and resid 3168 through 3172 Processing helix chain 'B' and resid 3189 through 3191 No H-bonds generated for 'chain 'B' and resid 3189 through 3191' Processing helix chain 'B' and resid 3192 through 3198 Processing helix chain 'B' and resid 3202 through 3218 Processing helix chain 'B' and resid 3222 through 3234 Processing helix chain 'B' and resid 3235 through 3239 removed outlier: 3.754A pdb=" N SER B3238 " --> pdb=" O SER B3235 " (cutoff:3.500A) Processing helix chain 'B' and resid 3245 through 3257 Processing helix chain 'B' and resid 3259 through 3269 Processing helix chain 'B' and resid 3270 through 3285 removed outlier: 3.562A pdb=" N TYR B3274 " --> pdb=" O GLN B3270 " (cutoff:3.500A) Processing helix chain 'B' and resid 3286 through 3289 Processing helix chain 'B' and resid 3292 through 3315 Processing helix chain 'B' and resid 3317 through 3327 Processing helix chain 'B' and resid 3331 through 3344 Processing helix chain 'B' and resid 3350 through 3368 Processing helix chain 'B' and resid 3371 through 3383 Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 325 through 333 Processing helix chain 'D' and resid 336 through 349 Processing helix chain 'D' and resid 399 through 403 Processing helix chain 'D' and resid 425 through 446 Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 470 through 472 No H-bonds generated for 'chain 'D' and resid 470 through 472' Processing helix chain 'D' and resid 496 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 2921 through 2925 Processing sheet with id=AA2, first strand: chain 'A' and resid 2921 through 2925 Processing sheet with id=AA3, first strand: chain 'A' and resid 2939 through 2941 Processing sheet with id=AA4, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AA5, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AA6, first strand: chain 'C' and resid 270 through 272 966 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4926 1.34 - 1.46: 3174 1.46 - 1.58: 6926 1.58 - 1.70: 0 1.70 - 1.82: 158 Bond restraints: 15184 Sorted by residual: bond pdb=" CA PRO C 280 " pdb=" C PRO C 280 " ideal model delta sigma weight residual 1.514 1.507 0.007 5.50e-03 3.31e+04 1.75e+00 bond pdb=" CB ILE A2488 " pdb=" CG2 ILE A2488 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.97e-01 bond pdb=" CA VAL A2538 " pdb=" CB VAL A2538 " ideal model delta sigma weight residual 1.540 1.553 -0.013 1.36e-02 5.41e+03 8.52e-01 bond pdb=" CG LEU C 331 " pdb=" CD1 LEU C 331 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.94e-01 bond pdb=" CB MET D 492 " pdb=" CG MET D 492 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.91e-01 ... (remaining 15179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 20408 2.32 - 4.64: 138 4.64 - 6.96: 20 6.96 - 9.28: 3 9.28 - 11.60: 1 Bond angle restraints: 20570 Sorted by residual: angle pdb=" CB MET D 492 " pdb=" CG MET D 492 " pdb=" SD MET D 492 " ideal model delta sigma weight residual 112.70 124.30 -11.60 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C SER A2537 " pdb=" N VAL A2538 " pdb=" CA VAL A2538 " ideal model delta sigma weight residual 121.97 126.82 -4.85 1.80e+00 3.09e-01 7.27e+00 angle pdb=" CB MET C 492 " pdb=" CG MET C 492 " pdb=" SD MET C 492 " ideal model delta sigma weight residual 112.70 120.68 -7.98 3.00e+00 1.11e-01 7.08e+00 angle pdb=" CB MET A2662 " pdb=" CG MET A2662 " pdb=" SD MET A2662 " ideal model delta sigma weight residual 112.70 105.51 7.19 3.00e+00 1.11e-01 5.75e+00 angle pdb=" C PRO B2917 " pdb=" N LEU B2918 " pdb=" CA LEU B2918 " ideal model delta sigma weight residual 121.80 127.63 -5.83 2.44e+00 1.68e-01 5.71e+00 ... (remaining 20565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 8035 17.78 - 35.56: 960 35.56 - 53.34: 259 53.34 - 71.12: 63 71.12 - 88.90: 21 Dihedral angle restraints: 9338 sinusoidal: 3734 harmonic: 5604 Sorted by residual: dihedral pdb=" CA SER A3188 " pdb=" C SER A3188 " pdb=" N ASN A3189 " pdb=" CA ASN A3189 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA SER B3188 " pdb=" C SER B3188 " pdb=" N ASN B3189 " pdb=" CA ASN B3189 " ideal model delta harmonic sigma weight residual -180.00 -152.71 -27.29 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ASN B3189 " pdb=" C ASN B3189 " pdb=" N PRO B3190 " pdb=" CA PRO B3190 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 9335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2057 0.050 - 0.100: 341 0.100 - 0.150: 36 0.150 - 0.201: 1 0.201 - 0.251: 1 Chirality restraints: 2436 Sorted by residual: chirality pdb=" CB VAL A2538 " pdb=" CA VAL A2538 " pdb=" CG1 VAL A2538 " pdb=" CG2 VAL A2538 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU B2493 " pdb=" CB LEU B2493 " pdb=" CD1 LEU B2493 " pdb=" CD2 LEU B2493 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA ILE C 276 " pdb=" N ILE C 276 " pdb=" C ILE C 276 " pdb=" CB ILE C 276 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 2433 not shown) Planarity restraints: 2606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A3240 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A3241 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A3241 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A3241 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B3240 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B3241 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B3241 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B3241 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A2945 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A2946 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A2946 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A2946 " 0.022 5.00e-02 4.00e+02 ... (remaining 2603 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 5962 2.93 - 3.42: 15339 3.42 - 3.91: 24347 3.91 - 4.41: 26988 4.41 - 4.90: 45183 Nonbonded interactions: 117819 Sorted by model distance: nonbonded pdb=" O THR A2479 " pdb=" OD1 ASP A2483 " model vdw 2.434 3.040 nonbonded pdb=" O THR B2479 " pdb=" OD1 ASP B2483 " model vdw 2.438 3.040 nonbonded pdb=" C SER A3027 " pdb=" OG SER A3027 " model vdw 2.616 2.616 nonbonded pdb=" C SER B3027 " pdb=" OG SER B3027 " model vdw 2.616 2.616 nonbonded pdb=" N GLU B2480 " pdb=" OE1 GLU B2480 " model vdw 2.618 3.120 ... (remaining 117814 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.970 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.003 0.031 15192 Z= 0.129 Angle : 0.531 11.596 20582 Z= 0.276 Chirality : 0.037 0.251 2436 Planarity : 0.004 0.051 2606 Dihedral : 17.205 88.897 5670 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.44 % Allowed : 19.10 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.20), residues: 1872 helix: 2.70 (0.15), residues: 1240 sheet: None (None), residues: 0 loop : -0.34 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 422 TYR 0.011 0.001 TYR B2985 PHE 0.017 0.001 PHE A2947 TRP 0.006 0.001 TRP A3162 HIS 0.006 0.001 HIS A2579 Details of bonding type rmsd covalent geometry : bond 0.00289 (15184) covalent geometry : angle 0.53043 (20570) hydrogen bonds : bond 0.13154 ( 958) hydrogen bonds : angle 4.60884 ( 2835) metal coordination : bond 0.00173 ( 8) metal coordination : angle 1.45319 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 2542 LEU cc_start: 0.7991 (mm) cc_final: 0.7791 (mp) REVERT: A 3131 MET cc_start: 0.9072 (mmm) cc_final: 0.8788 (mmm) REVERT: C 279 TYR cc_start: 0.9165 (m-80) cc_final: 0.8840 (m-10) REVERT: C 347 MET cc_start: 0.8888 (ttp) cc_final: 0.8409 (ttm) REVERT: C 434 MET cc_start: 0.9006 (mmp) cc_final: 0.8708 (mmm) REVERT: B 2454 MET cc_start: 0.7390 (ttm) cc_final: 0.6890 (ttm) REVERT: B 2974 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8164 (tp40) REVERT: B 3131 MET cc_start: 0.9018 (mmm) cc_final: 0.8673 (mmm) REVERT: B 3301 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: B 3346 MET cc_start: 0.9009 (mmm) cc_final: 0.8483 (mtp) REVERT: D 279 TYR cc_start: 0.9194 (m-80) cc_final: 0.8847 (m-10) outliers start: 24 outliers final: 20 residues processed: 194 average time/residue: 0.6903 time to fit residues: 146.2740 Evaluate side-chains 189 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2560 GLU Chi-restraints excluded: chain A residue 2688 THR Chi-restraints excluded: chain A residue 2876 CYS Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3369 CYS Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain B residue 2472 VAL Chi-restraints excluded: chain B residue 2493 LEU Chi-restraints excluded: chain B residue 2494 ILE Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2688 THR Chi-restraints excluded: chain B residue 2876 CYS Chi-restraints excluded: chain B residue 2945 LEU Chi-restraints excluded: chain B residue 2974 GLN Chi-restraints excluded: chain B residue 2997 LYS Chi-restraints excluded: chain B residue 3119 ASP Chi-restraints excluded: chain B residue 3301 GLU Chi-restraints excluded: chain B residue 3330 ASP Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3369 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2555 ASN A2983 ASN C 424 GLN C 491 ASN B2555 ASN B3261 ASN B3292 ASN D 421 GLN D 424 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083640 restraints weight = 20848.554| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.12 r_work: 0.2921 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15192 Z= 0.134 Angle : 0.492 6.437 20582 Z= 0.251 Chirality : 0.037 0.180 2436 Planarity : 0.004 0.049 2606 Dihedral : 6.005 128.316 2069 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.17 % Allowed : 17.49 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.20), residues: 1872 helix: 2.89 (0.15), residues: 1262 sheet: None (None), residues: 0 loop : -0.34 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2680 TYR 0.008 0.001 TYR A2452 PHE 0.022 0.001 PHE B2678 TRP 0.007 0.001 TRP B3169 HIS 0.006 0.001 HIS B2579 Details of bonding type rmsd covalent geometry : bond 0.00314 (15184) covalent geometry : angle 0.49034 (20570) hydrogen bonds : bond 0.05058 ( 958) hydrogen bonds : angle 3.75239 ( 2835) metal coordination : bond 0.00185 ( 8) metal coordination : angle 1.52639 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 0.625 Fit side-chains REVERT: A 2483 ASP cc_start: 0.8356 (m-30) cc_final: 0.8140 (m-30) REVERT: A 2542 LEU cc_start: 0.7955 (mm) cc_final: 0.7741 (mp) REVERT: A 2680 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8022 (ptm160) REVERT: A 2973 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8050 (mp10) REVERT: A 3131 MET cc_start: 0.9012 (mmm) cc_final: 0.8668 (mmm) REVERT: A 3301 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: C 279 TYR cc_start: 0.9190 (m-80) cc_final: 0.8854 (m-10) REVERT: C 324 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8322 (mppt) REVERT: C 347 MET cc_start: 0.8852 (ttp) cc_final: 0.8442 (ttm) REVERT: B 2454 MET cc_start: 0.7334 (ttm) cc_final: 0.6928 (ttm) REVERT: B 2483 ASP cc_start: 0.8380 (m-30) cc_final: 0.8152 (m-30) REVERT: B 2542 LEU cc_start: 0.7626 (mm) cc_final: 0.7368 (mp) REVERT: B 2680 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7999 (ptm160) REVERT: B 2973 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8008 (mp10) REVERT: B 2997 LYS cc_start: 0.8643 (tptm) cc_final: 0.8239 (tptt) REVERT: B 3346 MET cc_start: 0.9066 (mmm) cc_final: 0.8563 (mtp) REVERT: D 279 TYR cc_start: 0.9191 (m-80) cc_final: 0.8880 (m-10) REVERT: D 325 ASP cc_start: 0.7652 (t0) cc_final: 0.7451 (t0) REVERT: D 332 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8377 (mttp) outliers start: 53 outliers final: 19 residues processed: 215 average time/residue: 0.6894 time to fit residues: 162.0289 Evaluate side-chains 195 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2457 LEU Chi-restraints excluded: chain A residue 2458 LEU Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2528 LEU Chi-restraints excluded: chain A residue 2534 ARG Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain A residue 2680 ARG Chi-restraints excluded: chain A residue 2688 THR Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain A residue 2973 GLN Chi-restraints excluded: chain A residue 3301 GLU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain B residue 2470 LYS Chi-restraints excluded: chain B residue 2472 VAL Chi-restraints excluded: chain B residue 2578 LEU Chi-restraints excluded: chain B residue 2675 SER Chi-restraints excluded: chain B residue 2680 ARG Chi-restraints excluded: chain B residue 2688 THR Chi-restraints excluded: chain B residue 2945 LEU Chi-restraints excluded: chain B residue 2973 GLN Chi-restraints excluded: chain B residue 2982 LEU Chi-restraints excluded: chain B residue 2991 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 332 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 chunk 158 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 89 optimal weight: 0.0040 chunk 186 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2475 HIS A2555 ASN C 424 GLN B2555 ASN B3292 ASN D 421 GLN D 424 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.084245 restraints weight = 20712.341| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.13 r_work: 0.2916 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15192 Z= 0.101 Angle : 0.447 7.239 20582 Z= 0.227 Chirality : 0.035 0.158 2436 Planarity : 0.003 0.048 2606 Dihedral : 3.907 28.652 2034 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.35 % Allowed : 18.08 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.20), residues: 1872 helix: 3.00 (0.15), residues: 1262 sheet: None (None), residues: 0 loop : -0.33 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 472 TYR 0.008 0.001 TYR A2912 PHE 0.011 0.001 PHE A2947 TRP 0.006 0.001 TRP C 409 HIS 0.004 0.001 HIS A2475 Details of bonding type rmsd covalent geometry : bond 0.00223 (15184) covalent geometry : angle 0.44612 (20570) hydrogen bonds : bond 0.04199 ( 958) hydrogen bonds : angle 3.57604 ( 2835) metal coordination : bond 0.00182 ( 8) metal coordination : angle 1.36911 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 2483 ASP cc_start: 0.8373 (m-30) cc_final: 0.8157 (m-30) REVERT: A 2973 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8008 (mp10) REVERT: A 2974 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: A 3131 MET cc_start: 0.9023 (mmm) cc_final: 0.8616 (mmm) REVERT: A 3301 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: C 279 TYR cc_start: 0.9166 (m-80) cc_final: 0.8817 (m-10) REVERT: C 331 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8638 (mp) REVERT: C 347 MET cc_start: 0.8737 (ttp) cc_final: 0.8416 (ttm) REVERT: C 449 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8386 (mp) REVERT: B 2483 ASP cc_start: 0.8254 (m-30) cc_final: 0.7935 (m-30) REVERT: B 2542 LEU cc_start: 0.7802 (mm) cc_final: 0.7548 (mp) REVERT: B 2997 LYS cc_start: 0.8626 (tptm) cc_final: 0.8248 (tptt) REVERT: B 3346 MET cc_start: 0.9020 (mmm) cc_final: 0.8503 (mtp) REVERT: D 279 TYR cc_start: 0.9190 (m-80) cc_final: 0.8875 (m-10) REVERT: D 325 ASP cc_start: 0.7712 (t0) cc_final: 0.7414 (t0) REVERT: D 332 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8339 (mttp) outliers start: 56 outliers final: 22 residues processed: 217 average time/residue: 0.6757 time to fit residues: 160.2712 Evaluate side-chains 201 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2457 LEU Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain A residue 2595 CYS Chi-restraints excluded: chain A residue 2680 ARG Chi-restraints excluded: chain A residue 2688 THR Chi-restraints excluded: chain A residue 2876 CYS Chi-restraints excluded: chain A residue 2973 GLN Chi-restraints excluded: chain A residue 2974 GLN Chi-restraints excluded: chain A residue 3027 SER Chi-restraints excluded: chain A residue 3119 ASP Chi-restraints excluded: chain A residue 3301 GLU Chi-restraints excluded: chain A residue 3330 ASP Chi-restraints excluded: chain A residue 3369 CYS Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain B residue 2470 LYS Chi-restraints excluded: chain B residue 2472 VAL Chi-restraints excluded: chain B residue 2578 LEU Chi-restraints excluded: chain B residue 2680 ARG Chi-restraints excluded: chain B residue 2688 THR Chi-restraints excluded: chain B residue 2876 CYS Chi-restraints excluded: chain B residue 2982 LEU Chi-restraints excluded: chain B residue 2991 VAL Chi-restraints excluded: chain B residue 3119 ASP Chi-restraints excluded: chain B residue 3369 CYS Chi-restraints excluded: chain D residue 332 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 169 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2475 HIS A2555 ASN B2555 ASN B3292 ASN D 421 GLN D 424 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.083332 restraints weight = 20611.579| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.12 r_work: 0.2903 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15192 Z= 0.114 Angle : 0.461 7.291 20582 Z= 0.232 Chirality : 0.035 0.145 2436 Planarity : 0.004 0.049 2606 Dihedral : 3.765 27.913 2030 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.65 % Allowed : 17.60 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.20), residues: 1872 helix: 3.03 (0.15), residues: 1262 sheet: None (None), residues: 0 loop : -0.31 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 472 TYR 0.008 0.001 TYR B2912 PHE 0.012 0.001 PHE B2678 TRP 0.006 0.001 TRP C 409 HIS 0.006 0.001 HIS A2579 Details of bonding type rmsd covalent geometry : bond 0.00266 (15184) covalent geometry : angle 0.45951 (20570) hydrogen bonds : bond 0.04376 ( 958) hydrogen bonds : angle 3.53519 ( 2835) metal coordination : bond 0.00153 ( 8) metal coordination : angle 1.33448 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 0.544 Fit side-chains REVERT: A 2477 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7391 (mm-40) REVERT: A 2483 ASP cc_start: 0.8375 (m-30) cc_final: 0.8121 (m-30) REVERT: A 2498 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7509 (ppp) REVERT: A 2973 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: A 2974 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8581 (tt0) REVERT: C 279 TYR cc_start: 0.9184 (m-80) cc_final: 0.8830 (m-10) REVERT: C 331 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8615 (mp) REVERT: C 347 MET cc_start: 0.8769 (ttp) cc_final: 0.8449 (ttm) REVERT: C 449 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8423 (mp) REVERT: B 2477 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7591 (mm-40) REVERT: B 2483 ASP cc_start: 0.8253 (m-30) cc_final: 0.7907 (m-30) REVERT: B 2542 LEU cc_start: 0.7833 (mm) cc_final: 0.7586 (mp) REVERT: B 2973 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7969 (mp10) REVERT: B 2997 LYS cc_start: 0.8646 (tptm) cc_final: 0.8271 (tptt) REVERT: B 3346 MET cc_start: 0.9065 (mmm) cc_final: 0.8568 (mtp) REVERT: D 279 TYR cc_start: 0.9202 (m-80) cc_final: 0.8858 (m-10) REVERT: D 325 ASP cc_start: 0.7888 (t0) cc_final: 0.7637 (t0) REVERT: D 332 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8349 (mttp) REVERT: D 490 VAL cc_start: 0.8831 (p) cc_final: 0.8585 (m) outliers start: 61 outliers final: 30 residues processed: 218 average time/residue: 0.6636 time to fit residues: 158.4223 Evaluate side-chains 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2457 LEU Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 GLN Chi-restraints excluded: chain A residue 2478 LEU Chi-restraints excluded: chain A residue 2494 ILE Chi-restraints excluded: chain A residue 2498 MET Chi-restraints excluded: chain A residue 2542 LEU Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain A residue 2680 ARG Chi-restraints excluded: chain A residue 2688 THR Chi-restraints excluded: chain A residue 2876 CYS Chi-restraints excluded: chain A residue 2940 MET Chi-restraints excluded: chain A residue 2973 GLN Chi-restraints excluded: chain A residue 2974 GLN Chi-restraints excluded: chain A residue 3027 SER Chi-restraints excluded: chain A residue 3074 LEU Chi-restraints excluded: chain A residue 3227 LEU Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3369 CYS Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain B residue 2470 LYS Chi-restraints excluded: chain B residue 2472 VAL Chi-restraints excluded: chain B residue 2477 GLN Chi-restraints excluded: chain B residue 2478 LEU Chi-restraints excluded: chain B residue 2578 LEU Chi-restraints excluded: chain B residue 2675 SER Chi-restraints excluded: chain B residue 2680 ARG Chi-restraints excluded: chain B residue 2688 THR Chi-restraints excluded: chain B residue 2876 CYS Chi-restraints excluded: chain B residue 2973 GLN Chi-restraints excluded: chain B residue 2982 LEU Chi-restraints excluded: chain B residue 2991 VAL Chi-restraints excluded: chain B residue 3119 ASP Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3369 CYS Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 332 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 85 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 2 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2475 HIS A2983 ASN C 424 GLN B2555 ASN B3292 ASN D 421 GLN D 424 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.083914 restraints weight = 20612.639| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.15 r_work: 0.2913 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15192 Z= 0.099 Angle : 0.448 7.337 20582 Z= 0.226 Chirality : 0.035 0.154 2436 Planarity : 0.003 0.047 2606 Dihedral : 3.706 27.065 2030 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.53 % Allowed : 17.96 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.20), residues: 1872 helix: 3.11 (0.15), residues: 1262 sheet: None (None), residues: 0 loop : -0.30 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2570 TYR 0.009 0.001 TYR A2912 PHE 0.012 0.001 PHE A2947 TRP 0.005 0.001 TRP C 409 HIS 0.005 0.001 HIS A2475 Details of bonding type rmsd covalent geometry : bond 0.00221 (15184) covalent geometry : angle 0.44708 (20570) hydrogen bonds : bond 0.04016 ( 958) hydrogen bonds : angle 3.48391 ( 2835) metal coordination : bond 0.00169 ( 8) metal coordination : angle 1.32647 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 0.632 Fit side-chains REVERT: A 2477 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7415 (mm-40) REVERT: A 2483 ASP cc_start: 0.8364 (m-30) cc_final: 0.8080 (m-30) REVERT: A 2973 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: A 2974 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: A 3285 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7743 (ptpp) REVERT: A 3301 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: A 3369 CYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6942 (p) REVERT: C 279 TYR cc_start: 0.9168 (m-80) cc_final: 0.8809 (m-10) REVERT: C 325 ASP cc_start: 0.7434 (t0) cc_final: 0.7146 (t0) REVERT: C 331 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8598 (mp) REVERT: C 434 MET cc_start: 0.8855 (mmp) cc_final: 0.8516 (mmm) REVERT: C 449 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8408 (mp) REVERT: B 2459 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8263 (tp40) REVERT: B 2477 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7561 (mm-40) REVERT: B 2483 ASP cc_start: 0.8258 (m-30) cc_final: 0.7883 (m-30) REVERT: B 2542 LEU cc_start: 0.7810 (mm) cc_final: 0.7573 (mp) REVERT: B 2973 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7929 (mp10) REVERT: B 2997 LYS cc_start: 0.8632 (tptm) cc_final: 0.8256 (tptt) REVERT: B 3346 MET cc_start: 0.9063 (mmm) cc_final: 0.8565 (mtp) REVERT: D 279 TYR cc_start: 0.9180 (m-80) cc_final: 0.8825 (m-10) REVERT: D 325 ASP cc_start: 0.7865 (t0) cc_final: 0.7589 (t0) REVERT: D 332 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8306 (mttp) REVERT: D 490 VAL cc_start: 0.8815 (p) cc_final: 0.8577 (m) outliers start: 59 outliers final: 31 residues processed: 219 average time/residue: 0.6629 time to fit residues: 158.8744 Evaluate side-chains 214 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 GLN Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2528 LEU Chi-restraints excluded: chain A residue 2534 ARG Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain A residue 2595 CYS Chi-restraints excluded: chain A residue 2680 ARG Chi-restraints excluded: chain A residue 2688 THR Chi-restraints excluded: chain A residue 2876 CYS Chi-restraints excluded: chain A residue 2940 MET Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain A residue 2973 GLN Chi-restraints excluded: chain A residue 2974 GLN Chi-restraints excluded: chain A residue 3027 SER Chi-restraints excluded: chain A residue 3074 LEU Chi-restraints excluded: chain A residue 3227 LEU Chi-restraints excluded: chain A residue 3285 LYS Chi-restraints excluded: chain A residue 3301 GLU Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3369 CYS Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain B residue 2459 GLN Chi-restraints excluded: chain B residue 2470 LYS Chi-restraints excluded: chain B residue 2472 VAL Chi-restraints excluded: chain B residue 2477 GLN Chi-restraints excluded: chain B residue 2493 LEU Chi-restraints excluded: chain B residue 2578 LEU Chi-restraints excluded: chain B residue 2675 SER Chi-restraints excluded: chain B residue 2680 ARG Chi-restraints excluded: chain B residue 2688 THR Chi-restraints excluded: chain B residue 2876 CYS Chi-restraints excluded: chain B residue 2973 GLN Chi-restraints excluded: chain B residue 2982 LEU Chi-restraints excluded: chain B residue 2991 VAL Chi-restraints excluded: chain B residue 3027 SER Chi-restraints excluded: chain B residue 3119 ASP Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3369 CYS Chi-restraints excluded: chain D residue 332 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2475 HIS C 424 GLN B2555 ASN B3292 ASN D 421 GLN D 424 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.082233 restraints weight = 20641.541| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.14 r_work: 0.2885 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15192 Z= 0.133 Angle : 0.484 8.192 20582 Z= 0.243 Chirality : 0.036 0.156 2436 Planarity : 0.004 0.047 2606 Dihedral : 3.776 27.333 2030 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.47 % Allowed : 18.86 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.20), residues: 1872 helix: 3.05 (0.14), residues: 1262 sheet: None (None), residues: 0 loop : -0.32 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 472 TYR 0.009 0.001 TYR A2912 PHE 0.014 0.001 PHE B2678 TRP 0.006 0.001 TRP C 409 HIS 0.007 0.001 HIS B2579 Details of bonding type rmsd covalent geometry : bond 0.00318 (15184) covalent geometry : angle 0.48287 (20570) hydrogen bonds : bond 0.04633 ( 958) hydrogen bonds : angle 3.52036 ( 2835) metal coordination : bond 0.00134 ( 8) metal coordination : angle 1.27566 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 2477 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7466 (mm-40) REVERT: A 2483 ASP cc_start: 0.8265 (m-30) cc_final: 0.7985 (m-30) REVERT: A 2490 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8062 (ttmm) REVERT: A 2973 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: A 2974 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8586 (tt0) REVERT: A 3285 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7835 (ptpp) REVERT: A 3301 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: C 279 TYR cc_start: 0.9181 (m-80) cc_final: 0.8803 (m-10) REVERT: C 325 ASP cc_start: 0.7437 (t0) cc_final: 0.7207 (t0) REVERT: C 331 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8501 (mp) REVERT: C 449 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 2459 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8303 (tp40) REVERT: B 2477 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7541 (mm-40) REVERT: B 2483 ASP cc_start: 0.8250 (m-30) cc_final: 0.7866 (m-30) REVERT: B 2542 LEU cc_start: 0.7830 (mm) cc_final: 0.7595 (mp) REVERT: B 2973 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: B 2997 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8284 (tptt) REVERT: B 3346 MET cc_start: 0.9045 (mmm) cc_final: 0.8518 (mtp) REVERT: D 279 TYR cc_start: 0.9193 (m-80) cc_final: 0.8815 (m-10) REVERT: D 325 ASP cc_start: 0.7783 (t0) cc_final: 0.7507 (t0) REVERT: D 332 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8294 (mttp) REVERT: D 490 VAL cc_start: 0.8838 (p) cc_final: 0.8609 (m) outliers start: 58 outliers final: 31 residues processed: 209 average time/residue: 0.6532 time to fit residues: 149.5652 Evaluate side-chains 214 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 GLN Chi-restraints excluded: chain A residue 2490 LYS Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2494 ILE Chi-restraints excluded: chain A residue 2528 LEU Chi-restraints excluded: chain A residue 2534 ARG Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain A residue 2680 ARG Chi-restraints excluded: chain A residue 2688 THR Chi-restraints excluded: chain A residue 2876 CYS Chi-restraints excluded: chain A residue 2940 MET Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain A residue 2973 GLN Chi-restraints excluded: chain A residue 2974 GLN Chi-restraints excluded: chain A residue 3027 SER Chi-restraints excluded: chain A residue 3074 LEU Chi-restraints excluded: chain A residue 3227 LEU Chi-restraints excluded: chain A residue 3285 LYS Chi-restraints excluded: chain A residue 3301 GLU Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3369 CYS Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain B residue 2459 GLN Chi-restraints excluded: chain B residue 2470 LYS Chi-restraints excluded: chain B residue 2472 VAL Chi-restraints excluded: chain B residue 2477 GLN Chi-restraints excluded: chain B residue 2493 LEU Chi-restraints excluded: chain B residue 2578 LEU Chi-restraints excluded: chain B residue 2675 SER Chi-restraints excluded: chain B residue 2680 ARG Chi-restraints excluded: chain B residue 2688 THR Chi-restraints excluded: chain B residue 2876 CYS Chi-restraints excluded: chain B residue 2945 LEU Chi-restraints excluded: chain B residue 2973 GLN Chi-restraints excluded: chain B residue 2991 VAL Chi-restraints excluded: chain B residue 2997 LYS Chi-restraints excluded: chain B residue 3027 SER Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3369 CYS Chi-restraints excluded: chain D residue 332 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 110 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 GLN B2555 ASN B3292 ASN D 421 GLN D 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.081950 restraints weight = 20557.833| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.11 r_work: 0.2880 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15192 Z= 0.133 Angle : 0.490 8.761 20582 Z= 0.246 Chirality : 0.036 0.150 2436 Planarity : 0.004 0.047 2606 Dihedral : 3.824 27.829 2030 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.23 % Allowed : 19.16 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.20), residues: 1872 helix: 3.03 (0.14), residues: 1262 sheet: None (None), residues: 0 loop : -0.33 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 472 TYR 0.009 0.001 TYR A2912 PHE 0.016 0.001 PHE A2947 TRP 0.006 0.001 TRP C 409 HIS 0.006 0.001 HIS B2579 Details of bonding type rmsd covalent geometry : bond 0.00318 (15184) covalent geometry : angle 0.48878 (20570) hydrogen bonds : bond 0.04705 ( 958) hydrogen bonds : angle 3.53387 ( 2835) metal coordination : bond 0.00172 ( 8) metal coordination : angle 1.32452 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.514 Fit side-chains REVERT: A 2477 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7492 (mm-40) REVERT: A 2483 ASP cc_start: 0.8225 (m-30) cc_final: 0.7916 (m-30) REVERT: A 2490 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8038 (ttmm) REVERT: A 2498 MET cc_start: 0.7674 (ppp) cc_final: 0.7443 (ppp) REVERT: A 2973 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: A 2974 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8593 (tt0) REVERT: A 3285 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7882 (ptpp) REVERT: A 3301 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: A 3369 CYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6961 (p) REVERT: C 279 TYR cc_start: 0.9176 (m-80) cc_final: 0.8786 (m-10) REVERT: C 325 ASP cc_start: 0.7456 (t0) cc_final: 0.7184 (t0) REVERT: C 331 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8481 (mp) REVERT: C 347 MET cc_start: 0.8853 (ttp) cc_final: 0.8505 (ttm) REVERT: B 2459 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8316 (tp40) REVERT: B 2477 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7453 (mm-40) REVERT: B 2483 ASP cc_start: 0.8245 (m-30) cc_final: 0.7863 (m-30) REVERT: B 2490 LYS cc_start: 0.8408 (ptmt) cc_final: 0.7947 (pptt) REVERT: B 2542 LEU cc_start: 0.7825 (mm) cc_final: 0.7597 (mp) REVERT: B 2947 PHE cc_start: 0.8084 (m-80) cc_final: 0.7884 (m-80) REVERT: B 2973 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: B 2997 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8270 (tptt) REVERT: B 3346 MET cc_start: 0.9056 (mmm) cc_final: 0.8537 (mtp) REVERT: D 279 TYR cc_start: 0.9192 (m-80) cc_final: 0.8808 (m-10) REVERT: D 325 ASP cc_start: 0.7760 (t0) cc_final: 0.7456 (t0) REVERT: D 332 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8306 (mttp) outliers start: 54 outliers final: 28 residues processed: 209 average time/residue: 0.6023 time to fit residues: 138.1560 Evaluate side-chains 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 GLN Chi-restraints excluded: chain A residue 2490 LYS Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2528 LEU Chi-restraints excluded: chain A residue 2534 ARG Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain A residue 2680 ARG Chi-restraints excluded: chain A residue 2688 THR Chi-restraints excluded: chain A residue 2876 CYS Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain A residue 2973 GLN Chi-restraints excluded: chain A residue 2974 GLN Chi-restraints excluded: chain A residue 3027 SER Chi-restraints excluded: chain A residue 3074 LEU Chi-restraints excluded: chain A residue 3227 LEU Chi-restraints excluded: chain A residue 3285 LYS Chi-restraints excluded: chain A residue 3301 GLU Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3369 CYS Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain B residue 2459 GLN Chi-restraints excluded: chain B residue 2470 LYS Chi-restraints excluded: chain B residue 2472 VAL Chi-restraints excluded: chain B residue 2477 GLN Chi-restraints excluded: chain B residue 2493 LEU Chi-restraints excluded: chain B residue 2578 LEU Chi-restraints excluded: chain B residue 2675 SER Chi-restraints excluded: chain B residue 2680 ARG Chi-restraints excluded: chain B residue 2688 THR Chi-restraints excluded: chain B residue 2876 CYS Chi-restraints excluded: chain B residue 2945 LEU Chi-restraints excluded: chain B residue 2973 GLN Chi-restraints excluded: chain B residue 2991 VAL Chi-restraints excluded: chain B residue 2997 LYS Chi-restraints excluded: chain B residue 3027 SER Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3369 CYS Chi-restraints excluded: chain D residue 332 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 30 optimal weight: 1.9990 chunk 160 optimal weight: 0.0060 chunk 134 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 GLN B2555 ASN B3292 ASN D 421 GLN D 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.082390 restraints weight = 20714.974| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.12 r_work: 0.2887 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15192 Z= 0.122 Angle : 0.490 9.687 20582 Z= 0.244 Chirality : 0.036 0.157 2436 Planarity : 0.003 0.047 2606 Dihedral : 3.808 27.319 2030 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.11 % Allowed : 19.70 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.20), residues: 1872 helix: 3.06 (0.14), residues: 1262 sheet: None (None), residues: 0 loop : -0.33 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 472 TYR 0.008 0.001 TYR A2912 PHE 0.012 0.001 PHE B2678 TRP 0.006 0.001 TRP C 409 HIS 0.006 0.001 HIS A2579 Details of bonding type rmsd covalent geometry : bond 0.00287 (15184) covalent geometry : angle 0.48865 (20570) hydrogen bonds : bond 0.04522 ( 958) hydrogen bonds : angle 3.51960 ( 2835) metal coordination : bond 0.00170 ( 8) metal coordination : angle 1.35151 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 0.411 Fit side-chains REVERT: A 2477 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7444 (mm-40) REVERT: A 2483 ASP cc_start: 0.8206 (m-30) cc_final: 0.7874 (m-30) REVERT: A 2498 MET cc_start: 0.7671 (ppp) cc_final: 0.7421 (ppp) REVERT: A 2973 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: A 2974 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: A 3285 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7860 (ptpp) REVERT: A 3301 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: A 3369 CYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6897 (p) REVERT: C 279 TYR cc_start: 0.9167 (m-80) cc_final: 0.8782 (m-10) REVERT: C 325 ASP cc_start: 0.7432 (t0) cc_final: 0.7144 (t0) REVERT: C 331 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8498 (mp) REVERT: C 347 MET cc_start: 0.8808 (ttp) cc_final: 0.8474 (ttm) REVERT: C 434 MET cc_start: 0.8952 (mmp) cc_final: 0.8583 (mmm) REVERT: B 2459 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8248 (tp40) REVERT: B 2477 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7523 (mm-40) REVERT: B 2483 ASP cc_start: 0.8244 (m-30) cc_final: 0.7846 (m-30) REVERT: B 2490 LYS cc_start: 0.8378 (ptmt) cc_final: 0.7952 (pptt) REVERT: B 2973 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: B 2997 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8263 (tptt) REVERT: B 3346 MET cc_start: 0.9044 (mmm) cc_final: 0.8522 (mtp) REVERT: D 267 GLN cc_start: 0.7492 (pt0) cc_final: 0.7061 (tt0) REVERT: D 279 TYR cc_start: 0.9186 (m-80) cc_final: 0.8804 (m-10) REVERT: D 325 ASP cc_start: 0.7743 (t0) cc_final: 0.7437 (t0) REVERT: D 332 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8283 (mttp) outliers start: 52 outliers final: 27 residues processed: 204 average time/residue: 0.6369 time to fit residues: 141.8070 Evaluate side-chains 208 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 GLN Chi-restraints excluded: chain A residue 2528 LEU Chi-restraints excluded: chain A residue 2534 ARG Chi-restraints excluded: chain A residue 2542 LEU Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain A residue 2680 ARG Chi-restraints excluded: chain A residue 2876 CYS Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain A residue 2973 GLN Chi-restraints excluded: chain A residue 2974 GLN Chi-restraints excluded: chain A residue 3027 SER Chi-restraints excluded: chain A residue 3074 LEU Chi-restraints excluded: chain A residue 3227 LEU Chi-restraints excluded: chain A residue 3285 LYS Chi-restraints excluded: chain A residue 3301 GLU Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3369 CYS Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain B residue 2459 GLN Chi-restraints excluded: chain B residue 2470 LYS Chi-restraints excluded: chain B residue 2472 VAL Chi-restraints excluded: chain B residue 2477 GLN Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2578 LEU Chi-restraints excluded: chain B residue 2680 ARG Chi-restraints excluded: chain B residue 2876 CYS Chi-restraints excluded: chain B residue 2945 LEU Chi-restraints excluded: chain B residue 2973 GLN Chi-restraints excluded: chain B residue 2991 VAL Chi-restraints excluded: chain B residue 2997 LYS Chi-restraints excluded: chain B residue 3027 SER Chi-restraints excluded: chain B residue 3119 ASP Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3369 CYS Chi-restraints excluded: chain D residue 332 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 183 optimal weight: 0.0970 chunk 155 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 GLN B2555 ASN B3292 ASN D 421 GLN D 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.112043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.083041 restraints weight = 20743.167| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.13 r_work: 0.2899 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15192 Z= 0.108 Angle : 0.482 10.386 20582 Z= 0.239 Chirality : 0.036 0.168 2436 Planarity : 0.003 0.047 2606 Dihedral : 3.696 27.422 2028 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.57 % Allowed : 20.30 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.20), residues: 1872 helix: 3.11 (0.14), residues: 1262 sheet: None (None), residues: 0 loop : -0.30 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 472 TYR 0.009 0.001 TYR A2912 PHE 0.017 0.001 PHE A2947 TRP 0.006 0.001 TRP C 409 HIS 0.005 0.001 HIS A2579 Details of bonding type rmsd covalent geometry : bond 0.00246 (15184) covalent geometry : angle 0.48098 (20570) hydrogen bonds : bond 0.04251 ( 958) hydrogen bonds : angle 3.49650 ( 2835) metal coordination : bond 0.00167 ( 8) metal coordination : angle 1.37102 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.705 Fit side-chains REVERT: A 2477 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7442 (mm-40) REVERT: A 2483 ASP cc_start: 0.8078 (m-30) cc_final: 0.7741 (m-30) REVERT: A 2498 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7414 (ppp) REVERT: A 2973 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: A 2974 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8562 (tt0) REVERT: A 3285 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7838 (ptpp) REVERT: A 3301 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: A 3369 CYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6812 (p) REVERT: C 279 TYR cc_start: 0.9160 (m-80) cc_final: 0.8778 (m-10) REVERT: C 325 ASP cc_start: 0.7398 (t0) cc_final: 0.7142 (t0) REVERT: C 331 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8482 (mp) REVERT: C 347 MET cc_start: 0.8782 (ttp) cc_final: 0.8478 (ttm) REVERT: C 434 MET cc_start: 0.8974 (mmp) cc_final: 0.8606 (mmm) REVERT: B 2477 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7493 (mm-40) REVERT: B 2483 ASP cc_start: 0.8038 (m-30) cc_final: 0.7664 (m-30) REVERT: B 2490 LYS cc_start: 0.8376 (ptmt) cc_final: 0.7936 (ptpp) REVERT: B 2973 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: B 2997 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8243 (tptt) REVERT: B 3301 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: B 3346 MET cc_start: 0.9069 (mmm) cc_final: 0.8560 (mtp) REVERT: D 267 GLN cc_start: 0.7540 (pt0) cc_final: 0.7145 (tt0) REVERT: D 279 TYR cc_start: 0.9184 (m-80) cc_final: 0.8806 (m-10) REVERT: D 325 ASP cc_start: 0.7735 (t0) cc_final: 0.7457 (t0) REVERT: D 332 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8279 (mttp) REVERT: D 345 GLU cc_start: 0.8079 (tt0) cc_final: 0.7699 (tm-30) outliers start: 43 outliers final: 26 residues processed: 204 average time/residue: 0.6799 time to fit residues: 151.2164 Evaluate side-chains 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 GLN Chi-restraints excluded: chain A residue 2498 MET Chi-restraints excluded: chain A residue 2528 LEU Chi-restraints excluded: chain A residue 2534 ARG Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain A residue 2680 ARG Chi-restraints excluded: chain A residue 2876 CYS Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain A residue 2973 GLN Chi-restraints excluded: chain A residue 2974 GLN Chi-restraints excluded: chain A residue 3027 SER Chi-restraints excluded: chain A residue 3074 LEU Chi-restraints excluded: chain A residue 3227 LEU Chi-restraints excluded: chain A residue 3285 LYS Chi-restraints excluded: chain A residue 3301 GLU Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3369 CYS Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain B residue 2470 LYS Chi-restraints excluded: chain B residue 2472 VAL Chi-restraints excluded: chain B residue 2477 GLN Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2578 LEU Chi-restraints excluded: chain B residue 2680 ARG Chi-restraints excluded: chain B residue 2876 CYS Chi-restraints excluded: chain B residue 2942 ILE Chi-restraints excluded: chain B residue 2945 LEU Chi-restraints excluded: chain B residue 2973 GLN Chi-restraints excluded: chain B residue 2991 VAL Chi-restraints excluded: chain B residue 2997 LYS Chi-restraints excluded: chain B residue 3027 SER Chi-restraints excluded: chain B residue 3119 ASP Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3301 GLU Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain B residue 3369 CYS Chi-restraints excluded: chain D residue 332 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 144 optimal weight: 3.9990 chunk 178 optimal weight: 0.0870 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 156 optimal weight: 5.9990 chunk 137 optimal weight: 0.3980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 GLN B2555 ASN B3292 ASN D 421 GLN D 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.083912 restraints weight = 20664.782| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.12 r_work: 0.2915 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15192 Z= 0.101 Angle : 0.473 11.556 20582 Z= 0.233 Chirality : 0.035 0.158 2436 Planarity : 0.003 0.048 2606 Dihedral : 3.642 27.073 2028 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.40 % Allowed : 20.54 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.20), residues: 1872 helix: 3.16 (0.15), residues: 1262 sheet: None (None), residues: 0 loop : -0.30 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 472 TYR 0.009 0.001 TYR A2912 PHE 0.007 0.001 PHE A2678 TRP 0.006 0.001 TRP A3193 HIS 0.005 0.001 HIS B3287 Details of bonding type rmsd covalent geometry : bond 0.00225 (15184) covalent geometry : angle 0.47218 (20570) hydrogen bonds : bond 0.03941 ( 958) hydrogen bonds : angle 3.45986 ( 2835) metal coordination : bond 0.00186 ( 8) metal coordination : angle 1.49462 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.643 Fit side-chains REVERT: A 2477 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7508 (mm-40) REVERT: A 2483 ASP cc_start: 0.8126 (m-30) cc_final: 0.7791 (m-30) REVERT: A 2498 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7375 (ppp) REVERT: A 2973 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: A 3285 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7777 (ptpp) REVERT: A 3301 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: A 3369 CYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6816 (p) REVERT: C 279 TYR cc_start: 0.9156 (m-80) cc_final: 0.8779 (m-10) REVERT: C 325 ASP cc_start: 0.7389 (t0) cc_final: 0.7130 (t0) REVERT: C 331 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8522 (mp) REVERT: C 347 MET cc_start: 0.8730 (ttp) cc_final: 0.8440 (ttm) REVERT: C 434 MET cc_start: 0.8878 (mmp) cc_final: 0.8511 (mmm) REVERT: B 2459 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8257 (tp40) REVERT: B 2477 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7486 (mm-40) REVERT: B 2483 ASP cc_start: 0.8012 (m-30) cc_final: 0.7703 (m-30) REVERT: B 2490 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7842 (pptt) REVERT: B 2973 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: B 2997 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8235 (tptt) REVERT: B 3301 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: B 3346 MET cc_start: 0.9035 (mmm) cc_final: 0.8524 (mtp) REVERT: D 279 TYR cc_start: 0.9177 (m-80) cc_final: 0.8805 (m-10) REVERT: D 325 ASP cc_start: 0.7711 (t0) cc_final: 0.7436 (t0) REVERT: D 332 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8287 (mttp) outliers start: 40 outliers final: 25 residues processed: 208 average time/residue: 0.6750 time to fit residues: 153.5110 Evaluate side-chains 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2472 VAL Chi-restraints excluded: chain A residue 2477 GLN Chi-restraints excluded: chain A residue 2498 MET Chi-restraints excluded: chain A residue 2528 LEU Chi-restraints excluded: chain A residue 2534 ARG Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain A residue 2680 ARG Chi-restraints excluded: chain A residue 2876 CYS Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain A residue 2973 GLN Chi-restraints excluded: chain A residue 3027 SER Chi-restraints excluded: chain A residue 3074 LEU Chi-restraints excluded: chain A residue 3227 LEU Chi-restraints excluded: chain A residue 3285 LYS Chi-restraints excluded: chain A residue 3301 GLU Chi-restraints excluded: chain A residue 3336 LEU Chi-restraints excluded: chain A residue 3369 CYS Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain B residue 2459 GLN Chi-restraints excluded: chain B residue 2470 LYS Chi-restraints excluded: chain B residue 2472 VAL Chi-restraints excluded: chain B residue 2477 GLN Chi-restraints excluded: chain B residue 2542 LEU Chi-restraints excluded: chain B residue 2578 LEU Chi-restraints excluded: chain B residue 2680 ARG Chi-restraints excluded: chain B residue 2876 CYS Chi-restraints excluded: chain B residue 2942 ILE Chi-restraints excluded: chain B residue 2945 LEU Chi-restraints excluded: chain B residue 2973 GLN Chi-restraints excluded: chain B residue 2991 VAL Chi-restraints excluded: chain B residue 2997 LYS Chi-restraints excluded: chain B residue 3027 SER Chi-restraints excluded: chain B residue 3119 ASP Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3301 GLU Chi-restraints excluded: chain B residue 3336 LEU Chi-restraints excluded: chain D residue 332 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 137 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3292 ASN C 424 GLN B2555 ASN B3292 ASN D 267 GLN D 421 GLN D 424 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083686 restraints weight = 20656.868| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.12 r_work: 0.2908 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15192 Z= 0.105 Angle : 0.480 11.485 20582 Z= 0.236 Chirality : 0.035 0.162 2436 Planarity : 0.003 0.047 2606 Dihedral : 3.625 27.166 2028 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.51 % Allowed : 20.54 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.20), residues: 1872 helix: 3.16 (0.14), residues: 1262 sheet: None (None), residues: 0 loop : -0.31 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B2534 TYR 0.009 0.001 TYR A2912 PHE 0.016 0.001 PHE A2947 TRP 0.005 0.001 TRP C 409 HIS 0.005 0.001 HIS B3287 Details of bonding type rmsd covalent geometry : bond 0.00241 (15184) covalent geometry : angle 0.47877 (20570) hydrogen bonds : bond 0.04031 ( 958) hydrogen bonds : angle 3.45396 ( 2835) metal coordination : bond 0.00135 ( 8) metal coordination : angle 1.24973 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5917.39 seconds wall clock time: 101 minutes 38.65 seconds (6098.65 seconds total)