Starting phenix.real_space_refine on Sun Apr 5 13:39:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mc4_63788/04_2026/9mc4_63788_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mc4_63788/04_2026/9mc4_63788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mc4_63788/04_2026/9mc4_63788_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mc4_63788/04_2026/9mc4_63788_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mc4_63788/04_2026/9mc4_63788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mc4_63788/04_2026/9mc4_63788.map" } resolution = 3.32 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= 0.010 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 P 1 5.49 5 S 51 5.16 5 C 6673 2.51 5 N 1797 2.21 5 O 1966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10488 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7785 Classifications: {'peptide': 987} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 933} Chain breaks: 1 Chain: "B" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 16, 'TRANS': 241} Chain breaks: 1 Chain: "C" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 608 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.47, per 1000 atoms: 0.24 Number of scatterers: 10488 At special positions: 0 Unit cell: (85.536, 100.44, 128.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 1 15.00 O 1966 8.00 N 1797 7.00 C 6673 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: 0.93 Conformation dependent library (CDL) restraints added in 462.5 milliseconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 49.1% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.822A pdb=" N VAL A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 108 through 114 removed outlier: 3.695A pdb=" N SER A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.915A pdb=" N ILE A 123 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.941A pdb=" N PHE A 323 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 344 removed outlier: 3.640A pdb=" N GLN A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 369 Processing helix chain 'A' and resid 379 through 390 removed outlier: 3.576A pdb=" N ILE A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.762A pdb=" N LEU A 445 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 4.270A pdb=" N VAL A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N SER A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ASP A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.735A pdb=" N LEU A 513 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 514 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.736A pdb=" N VAL A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.825A pdb=" N GLU A 557 " --> pdb=" O PRO A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.720A pdb=" N ASN A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 592 Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.737A pdb=" N SER A 621 " --> pdb=" O TYR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 637 removed outlier: 4.284A pdb=" N ASN A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 669 removed outlier: 3.607A pdb=" N THR A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Proline residue: A 659 - end of helix Processing helix chain 'A' and resid 671 through 678 Processing helix chain 'A' and resid 681 through 696 Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.938A pdb=" N CYS A 706 " --> pdb=" O THR A 702 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 707 " --> pdb=" O TRP A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 729 Processing helix chain 'A' and resid 758 through 776 removed outlier: 4.125A pdb=" N LEU A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 794 Processing helix chain 'A' and resid 825 through 833 Processing helix chain 'A' and resid 856 through 873 removed outlier: 4.460A pdb=" N ASP A 860 " --> pdb=" O ASN A 856 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 889 Processing helix chain 'A' and resid 894 through 915 removed outlier: 3.547A pdb=" N THR A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'A' and resid 971 through 983 removed outlier: 3.504A pdb=" N HIS A 983 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1012 removed outlier: 3.892A pdb=" N ASP A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1024 Processing helix chain 'B' and resid 950 through 969 Processing helix chain 'B' and resid 1041 through 1045 Processing helix chain 'B' and resid 1050 through 1054 Processing helix chain 'B' and resid 1060 through 1071 Processing helix chain 'B' and resid 1076 through 1081 removed outlier: 3.758A pdb=" N GLU B1081 " --> pdb=" O TYR B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1088 Processing helix chain 'B' and resid 1090 through 1118 Processing helix chain 'B' and resid 1120 through 1122 No H-bonds generated for 'chain 'B' and resid 1120 through 1122' Processing helix chain 'B' and resid 1123 through 1151 removed outlier: 3.896A pdb=" N HIS B1130 " --> pdb=" O GLU B1126 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B1132 " --> pdb=" O ARG B1128 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B1133 " --> pdb=" O GLN B1129 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP B1136 " --> pdb=" O SER B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1262 through 1283 removed outlier: 3.791A pdb=" N THR B1274 " --> pdb=" O ARG B1270 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B1283 " --> pdb=" O ALA B1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 147 removed outlier: 6.588A pdb=" N VAL A 99 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N TYR A 147 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 101 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER A 74 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL A 163 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A 76 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR A 165 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N SER A 78 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 266 removed outlier: 4.344A pdb=" N PHE A 247 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N THR A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 548 removed outlier: 6.174A pdb=" N ILE A 500 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N HIS A 548 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 502 " --> pdb=" O HIS A 548 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR A 471 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR A 503 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU A 473 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS A 470 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ALA A 572 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE A 472 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 598 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 945 through 947 Processing sheet with id=AA6, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.594A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL A1035 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN A 992 " --> pdb=" O VAL A1035 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A1037 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU A 990 " --> pdb=" O GLU A1037 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N CYS A1039 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN A 992 " --> pdb=" O MET A 996 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N MET A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.594A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS A1040 " --> pdb=" O VAL A1048 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 929 through 932 removed outlier: 3.576A pdb=" N SER B 930 " --> pdb=" O VAL B 975 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 978 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU B 984 " --> pdb=" O PHE B 978 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU B1003 " --> pdb=" O LEU B1022 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 17 removed outlier: 3.990A pdb=" N ARG C 42 " --> pdb=" O VAL C 70 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1389 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: 1.95 Time building geometry restraints manager: 1.19 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: 3445 1.34 - 1.46: 1562 1.46 - 1.58: 5635 1.58 - 1.70: 1 1.70 - 1.82: 80 Bond restraints: 10723 Sorted by residual: bond pdb=" N ASN A 228 " pdb=" CA ASN A 228 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.17e+00 bond pdb=" N MET A 766 " pdb=" CA MET A 766 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 6.03e+00 bond pdb=" N ASP A 227 " pdb=" CA ASP A 227 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.42e-02 4.96e+03 2.44e+00 bond pdb=" CA ASN A 228 " pdb=" C ASN A 228 " ideal model delta sigma weight residual 1.520 1.539 -0.019 1.23e-02 6.61e+03 2.38e+00 bond pdb=" N GLY A 230 " pdb=" CA GLY A 230 " ideal model delta sigma weight residual 1.449 1.470 -0.020 1.45e-02 4.76e+03 2.00e+00 ... (remaining 10718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 14236 1.90 - 3.81: 236 3.81 - 5.71: 51 5.71 - 7.61: 6 7.61 - 9.51: 7 Bond angle restraints: 14536 Sorted by residual: angle pdb=" N PRO A 229 " pdb=" CA PRO A 229 " pdb=" C PRO A 229 " ideal model delta sigma weight residual 112.47 121.98 -9.51 2.06e+00 2.36e-01 2.13e+01 angle pdb=" C GLY A 230 " pdb=" N VAL A 231 " pdb=" CA VAL A 231 " ideal model delta sigma weight residual 122.22 117.94 4.28 1.15e+00 7.56e-01 1.38e+01 angle pdb=" N CYS A 278 " pdb=" CA CYS A 278 " pdb=" C CYS A 278 " ideal model delta sigma weight residual 107.73 112.41 -4.68 1.34e+00 5.57e-01 1.22e+01 angle pdb=" CA ASP A 227 " pdb=" C ASP A 227 " pdb=" O ASP A 227 " ideal model delta sigma weight residual 121.05 117.65 3.40 1.05e+00 9.07e-01 1.05e+01 angle pdb=" CA ASP A 523 " pdb=" CB ASP A 523 " pdb=" CG ASP A 523 " ideal model delta sigma weight residual 112.60 115.72 -3.12 1.00e+00 1.00e+00 9.73e+00 ... (remaining 14531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5896 17.53 - 35.07: 404 35.07 - 52.60: 114 52.60 - 70.14: 34 70.14 - 87.67: 16 Dihedral angle restraints: 6464 sinusoidal: 2639 harmonic: 3825 Sorted by residual: dihedral pdb=" C4' AMP A1101 " pdb=" C5' AMP A1101 " pdb=" O5' AMP A1101 " pdb=" P AMP A1101 " ideal model delta sinusoidal sigma weight residual 180.00 99.87 80.13 1 2.00e+01 2.50e-03 1.99e+01 dihedral pdb=" CA PHE A 652 " pdb=" C PHE A 652 " pdb=" N GLU A 653 " pdb=" CA GLU A 653 " ideal model delta harmonic sigma weight residual 180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE B1259 " pdb=" C PHE B1259 " pdb=" N PRO B1260 " pdb=" CA PRO B1260 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 6461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1434 0.071 - 0.142: 161 0.142 - 0.212: 5 0.212 - 0.283: 2 0.283 - 0.354: 1 Chirality restraints: 1603 Sorted by residual: chirality pdb=" CA PRO A 229 " pdb=" N PRO A 229 " pdb=" C PRO A 229 " pdb=" CB PRO A 229 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CG LEU B1261 " pdb=" CB LEU B1261 " pdb=" CD1 LEU B1261 " pdb=" CD2 LEU B1261 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C3' AMP A1101 " pdb=" C2' AMP A1101 " pdb=" C4' AMP A1101 " pdb=" O3' AMP A1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1600 not shown) Planarity restraints: 1901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B1259 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.71e+00 pdb=" N PRO B1260 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B1260 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B1260 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 523 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASP A 523 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP A 523 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 524 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 652 " 0.017 2.00e-02 2.50e+03 1.19e-02 2.50e+00 pdb=" CG PHE A 652 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 652 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 652 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 652 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 652 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 652 " 0.009 2.00e-02 2.50e+03 ... (remaining 1898 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 3775 2.89 - 3.39: 10202 3.39 - 3.89: 17663 3.89 - 4.40: 20576 4.40 - 4.90: 34284 Nonbonded interactions: 86500 Sorted by model distance: nonbonded pdb=" O ASP A 523 " pdb=" OD1 ASP A 523 " model vdw 2.382 3.040 nonbonded pdb=" O ASN A 928 " pdb=" O LEU A 931 " model vdw 2.545 3.040 nonbonded pdb=" N ASP A 227 " pdb=" O ASP A 227 " model vdw 2.571 2.496 nonbonded pdb=" N ASP A1042 " pdb=" OD1 ASP A1042 " model vdw 2.574 3.120 nonbonded pdb=" N ASP A 562 " pdb=" OD1 ASP A 562 " model vdw 2.606 3.120 ... (remaining 86495 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.850 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 0.032 10723 Z= 0.137 Angle : 0.651 9.513 14536 Z= 0.332 Chirality : 0.044 0.354 1603 Planarity : 0.005 0.069 1901 Dihedral : 14.478 87.674 3996 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.26 % Allowed : 9.79 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.10 (0.23), residues: 1312 helix: 0.64 (0.22), residues: 544 sheet: -0.46 (0.36), residues: 209 loop : -0.13 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.013 0.001 TYR A 666 PHE 0.025 0.002 PHE A 652 TRP 0.012 0.001 TRP A 714 HIS 0.005 0.001 HIS A 858 Details of bonding type rmsd covalent geometry : bond 0.00273 (10723) covalent geometry : angle 0.65055 (14536) hydrogen bonds : bond 0.13931 ( 507) hydrogen bonds : angle 7.01959 ( 1389) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 182 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ASP cc_start: 0.8406 (m-30) cc_final: 0.7898 (m-30) REVERT: B 1273 LEU cc_start: 0.8433 (tp) cc_final: 0.8214 (mm) outliers start: 3 outliers final: 0 residues processed: 184 average time/residue: 0.1259 time to fit residues: 31.3224 Evaluate side-chains 115 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 573 ASN ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1130 HIS C 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.187394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118401 restraints weight = 13870.283| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.13 r_work: 0.3257 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10723 Z= 0.209 Angle : 0.662 9.196 14536 Z= 0.331 Chirality : 0.045 0.252 1603 Planarity : 0.005 0.053 1901 Dihedral : 5.248 61.144 1437 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.45 % Allowed : 9.88 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.25 (0.23), residues: 1312 helix: 0.81 (0.22), residues: 539 sheet: -0.36 (0.36), residues: 202 loop : -0.12 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 192 TYR 0.017 0.002 TYR A 471 PHE 0.022 0.002 PHE A 975 TRP 0.011 0.002 TRP A 714 HIS 0.006 0.001 HIS B1130 Details of bonding type rmsd covalent geometry : bond 0.00502 (10723) covalent geometry : angle 0.66217 (14536) hydrogen bonds : bond 0.04296 ( 507) hydrogen bonds : angle 5.18252 ( 1389) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 TYR cc_start: 0.7714 (m-80) cc_final: 0.7360 (m-80) REVERT: A 408 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 410 MET cc_start: 0.8520 (mmt) cc_final: 0.8288 (mmt) REVERT: A 1032 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7895 (ttm110) REVERT: B 1105 LEU cc_start: 0.8964 (pp) cc_final: 0.8646 (tt) REVERT: B 1106 ILE cc_start: 0.8997 (mt) cc_final: 0.8470 (mm) REVERT: B 1110 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8208 (mm-40) REVERT: B 1114 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8727 (mt0) outliers start: 28 outliers final: 17 residues processed: 145 average time/residue: 0.1074 time to fit residues: 22.1760 Evaluate side-chains 116 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1126 GLU Chi-restraints excluded: chain B residue 1130 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 712 HIS ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.196543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131631 restraints weight = 14004.763| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.40 r_work: 0.3538 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10723 Z= 0.153 Angle : 0.592 8.192 14536 Z= 0.296 Chirality : 0.043 0.220 1603 Planarity : 0.004 0.044 1901 Dihedral : 5.004 55.403 1437 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.53 % Allowed : 11.36 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.32 (0.24), residues: 1312 helix: 0.90 (0.22), residues: 540 sheet: -0.48 (0.36), residues: 212 loop : -0.02 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.012 0.001 TYR A 471 PHE 0.016 0.001 PHE A 975 TRP 0.010 0.001 TRP A 647 HIS 0.005 0.001 HIS B1130 Details of bonding type rmsd covalent geometry : bond 0.00357 (10723) covalent geometry : angle 0.59223 (14536) hydrogen bonds : bond 0.03836 ( 507) hydrogen bonds : angle 4.90222 ( 1389) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4043 (mmm) cc_final: 0.3636 (ppp) REVERT: A 273 TYR cc_start: 0.7934 (m-80) cc_final: 0.7613 (m-80) REVERT: A 408 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8123 (mm-30) REVERT: A 410 MET cc_start: 0.8544 (mmt) cc_final: 0.8292 (mmm) REVERT: A 1032 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7836 (ttm110) REVERT: B 1063 GLN cc_start: 0.7788 (mt0) cc_final: 0.7510 (mt0) REVERT: B 1084 PHE cc_start: 0.3935 (OUTLIER) cc_final: 0.3475 (m-80) REVERT: B 1105 LEU cc_start: 0.8999 (pp) cc_final: 0.8629 (tt) REVERT: B 1110 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8342 (mm-40) REVERT: B 1114 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8710 (tt0) REVERT: B 1254 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7536 (mt) REVERT: B 1273 LEU cc_start: 0.8845 (tp) cc_final: 0.8454 (mm) REVERT: B 1285 MET cc_start: 0.2374 (ppp) cc_final: 0.2012 (pmm) outliers start: 29 outliers final: 19 residues processed: 126 average time/residue: 0.1089 time to fit residues: 19.4266 Evaluate side-chains 119 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 974 MET Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1130 HIS Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain B residue 1258 LEU Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 97 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1130 HIS ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.195276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136591 restraints weight = 14009.846| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.07 r_work: 0.3580 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10723 Z= 0.150 Angle : 0.576 7.448 14536 Z= 0.286 Chirality : 0.042 0.201 1603 Planarity : 0.004 0.040 1901 Dihedral : 4.892 52.510 1437 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.36 % Allowed : 12.41 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.41 (0.24), residues: 1312 helix: 1.00 (0.23), residues: 541 sheet: -0.49 (0.35), residues: 212 loop : 0.02 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.011 0.001 TYR A 471 PHE 0.016 0.001 PHE A 975 TRP 0.023 0.001 TRP A 714 HIS 0.004 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00355 (10723) covalent geometry : angle 0.57566 (14536) hydrogen bonds : bond 0.03649 ( 507) hydrogen bonds : angle 4.73895 ( 1389) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.3928 (mmm) cc_final: 0.3586 (ppp) REVERT: A 273 TYR cc_start: 0.7828 (m-80) cc_final: 0.7498 (m-80) REVERT: A 408 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 410 MET cc_start: 0.8502 (mmt) cc_final: 0.8242 (mmm) REVERT: B 955 PHE cc_start: 0.7847 (m-80) cc_final: 0.7358 (m-80) REVERT: B 990 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8366 (mmmt) REVERT: B 1084 PHE cc_start: 0.3906 (OUTLIER) cc_final: 0.3414 (m-80) REVERT: B 1105 LEU cc_start: 0.9020 (pp) cc_final: 0.8667 (tt) REVERT: B 1110 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8383 (mm-40) REVERT: B 1114 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8713 (tt0) REVERT: B 1254 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7520 (mt) REVERT: B 1273 LEU cc_start: 0.8829 (tp) cc_final: 0.8450 (mm) REVERT: B 1285 MET cc_start: 0.2302 (ppp) cc_final: 0.1899 (pmm) outliers start: 27 outliers final: 18 residues processed: 124 average time/residue: 0.0975 time to fit residues: 17.6579 Evaluate side-chains 116 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 974 MET Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1130 HIS Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 97 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.192895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.137064 restraints weight = 14087.462| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.96 r_work: 0.3521 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10723 Z= 0.233 Angle : 0.628 7.438 14536 Z= 0.315 Chirality : 0.044 0.214 1603 Planarity : 0.004 0.041 1901 Dihedral : 5.073 50.920 1437 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.97 % Allowed : 12.41 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.21 (0.24), residues: 1312 helix: 0.85 (0.23), residues: 543 sheet: -0.70 (0.35), residues: 212 loop : -0.06 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.014 0.001 TYR A 471 PHE 0.025 0.002 PHE A 975 TRP 0.011 0.002 TRP A 647 HIS 0.014 0.001 HIS B1130 Details of bonding type rmsd covalent geometry : bond 0.00565 (10723) covalent geometry : angle 0.62829 (14536) hydrogen bonds : bond 0.03966 ( 507) hydrogen bonds : angle 4.87841 ( 1389) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4132 (mmm) cc_final: 0.3746 (ppp) REVERT: A 273 TYR cc_start: 0.7854 (m-80) cc_final: 0.7553 (m-80) REVERT: A 513 LEU cc_start: 0.4561 (OUTLIER) cc_final: 0.4117 (pp) REVERT: B 955 PHE cc_start: 0.7854 (m-80) cc_final: 0.7358 (m-80) REVERT: B 1084 PHE cc_start: 0.3993 (OUTLIER) cc_final: 0.3497 (m-80) REVERT: B 1105 LEU cc_start: 0.9034 (pp) cc_final: 0.8662 (tt) REVERT: B 1110 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8347 (mm110) REVERT: B 1114 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8728 (tt0) REVERT: B 1254 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7462 (mt) REVERT: B 1273 LEU cc_start: 0.8811 (tp) cc_final: 0.8513 (mm) REVERT: B 1285 MET cc_start: 0.2375 (ppp) cc_final: 0.1013 (pmm) REVERT: C 74 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7947 (tpp80) outliers start: 34 outliers final: 22 residues processed: 127 average time/residue: 0.1029 time to fit residues: 18.9941 Evaluate side-chains 119 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 974 MET Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1130 HIS Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 126 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 114 optimal weight: 30.0000 chunk 95 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.194652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.134652 restraints weight = 14130.610| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.11 r_work: 0.3576 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10723 Z= 0.131 Angle : 0.572 7.239 14536 Z= 0.286 Chirality : 0.042 0.183 1603 Planarity : 0.004 0.039 1901 Dihedral : 4.898 51.593 1437 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.71 % Allowed : 12.85 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.40 (0.24), residues: 1312 helix: 1.04 (0.23), residues: 541 sheet: -0.54 (0.36), residues: 203 loop : -0.04 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.012 0.001 TYR B1002 PHE 0.014 0.001 PHE A 975 TRP 0.021 0.001 TRP A 714 HIS 0.008 0.001 HIS B1130 Details of bonding type rmsd covalent geometry : bond 0.00305 (10723) covalent geometry : angle 0.57180 (14536) hydrogen bonds : bond 0.03505 ( 507) hydrogen bonds : angle 4.65271 ( 1389) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4035 (mmm) cc_final: 0.3690 (ppp) REVERT: A 115 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7830 (tp40) REVERT: A 273 TYR cc_start: 0.7816 (m-80) cc_final: 0.7500 (m-80) REVERT: A 513 LEU cc_start: 0.4330 (OUTLIER) cc_final: 0.3984 (pp) REVERT: B 955 PHE cc_start: 0.7776 (m-80) cc_final: 0.7370 (m-80) REVERT: B 1084 PHE cc_start: 0.3855 (OUTLIER) cc_final: 0.3250 (m-80) REVERT: B 1110 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8527 (mm-40) REVERT: B 1254 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7429 (mt) REVERT: B 1273 LEU cc_start: 0.8789 (tp) cc_final: 0.8428 (mm) REVERT: C 74 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7958 (tpp80) outliers start: 31 outliers final: 18 residues processed: 123 average time/residue: 0.1073 time to fit residues: 18.6191 Evaluate side-chains 113 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 974 MET Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 1.9990 chunk 97 optimal weight: 0.0370 chunk 113 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.187644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.128858 restraints weight = 14010.145| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.87 r_work: 0.3478 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 10723 Z= 0.348 Angle : 0.741 9.547 14536 Z= 0.371 Chirality : 0.048 0.261 1603 Planarity : 0.005 0.042 1901 Dihedral : 5.476 65.578 1437 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.43 % Rotamer: Outliers : 2.71 % Allowed : 13.99 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.09 (0.23), residues: 1312 helix: 0.68 (0.22), residues: 532 sheet: -0.90 (0.35), residues: 206 loop : -0.29 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 72 TYR 0.020 0.002 TYR A 471 PHE 0.036 0.003 PHE A 975 TRP 0.013 0.002 TRP A 647 HIS 0.011 0.002 HIS B1130 Details of bonding type rmsd covalent geometry : bond 0.00844 (10723) covalent geometry : angle 0.74140 (14536) hydrogen bonds : bond 0.04468 ( 507) hydrogen bonds : angle 5.07996 ( 1389) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4366 (mmm) cc_final: 0.3986 (ppp) REVERT: A 115 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8197 (tp40) REVERT: A 513 LEU cc_start: 0.4807 (OUTLIER) cc_final: 0.4172 (pp) REVERT: A 867 ASN cc_start: 0.7750 (m-40) cc_final: 0.7269 (m110) REVERT: B 1084 PHE cc_start: 0.4046 (OUTLIER) cc_final: 0.3439 (m-80) REVERT: B 1103 MET cc_start: 0.7793 (mmp) cc_final: 0.7113 (mmp) REVERT: B 1254 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7476 (mt) REVERT: B 1273 LEU cc_start: 0.8828 (tp) cc_final: 0.8434 (mm) REVERT: C 39 ASP cc_start: 0.8183 (m-30) cc_final: 0.7941 (m-30) outliers start: 31 outliers final: 19 residues processed: 122 average time/residue: 0.1038 time to fit residues: 18.0373 Evaluate side-chains 115 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain B residue 974 MET Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 3 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 117 optimal weight: 0.0770 chunk 96 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1130 HIS ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.194398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.135041 restraints weight = 14025.311| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.13 r_work: 0.3583 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10723 Z= 0.121 Angle : 0.604 12.077 14536 Z= 0.298 Chirality : 0.042 0.180 1603 Planarity : 0.004 0.039 1901 Dihedral : 4.977 57.966 1437 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.97 % Favored : 96.95 % Rotamer: Outliers : 1.75 % Allowed : 15.38 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.30 (0.24), residues: 1312 helix: 1.05 (0.23), residues: 529 sheet: -0.77 (0.35), residues: 203 loop : -0.09 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1107 TYR 0.014 0.001 TYR B1002 PHE 0.011 0.001 PHE A 323 TRP 0.019 0.001 TRP A 714 HIS 0.006 0.001 HIS B1130 Details of bonding type rmsd covalent geometry : bond 0.00277 (10723) covalent geometry : angle 0.60371 (14536) hydrogen bonds : bond 0.03469 ( 507) hydrogen bonds : angle 4.66793 ( 1389) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4277 (mmm) cc_final: 0.3913 (ppp) REVERT: A 115 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7759 (tp40) REVERT: A 513 LEU cc_start: 0.4259 (OUTLIER) cc_final: 0.3935 (pp) REVERT: B 955 PHE cc_start: 0.7719 (m-80) cc_final: 0.7347 (m-80) REVERT: B 1084 PHE cc_start: 0.3881 (OUTLIER) cc_final: 0.3253 (m-80) REVERT: B 1110 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8211 (mm110) REVERT: B 1254 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7475 (mt) REVERT: B 1273 LEU cc_start: 0.8758 (tp) cc_final: 0.8419 (mm) REVERT: C 65 SER cc_start: 0.8678 (m) cc_final: 0.8323 (p) outliers start: 20 outliers final: 12 residues processed: 117 average time/residue: 0.1132 time to fit residues: 18.6337 Evaluate side-chains 109 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain B residue 974 MET Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 87 optimal weight: 1.9990 chunk 29 optimal weight: 0.0020 chunk 60 optimal weight: 0.0170 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.5026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.194753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.135721 restraints weight = 14142.370| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.25 r_work: 0.3564 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10723 Z= 0.125 Angle : 0.606 13.521 14536 Z= 0.302 Chirality : 0.043 0.188 1603 Planarity : 0.004 0.040 1901 Dihedral : 4.826 57.886 1437 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 1.49 % Allowed : 15.47 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.46 (0.24), residues: 1312 helix: 1.14 (0.23), residues: 530 sheet: -0.57 (0.36), residues: 203 loop : -0.01 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.012 0.001 TYR B1002 PHE 0.012 0.001 PHE A 323 TRP 0.021 0.002 TRP A 714 HIS 0.002 0.001 HIS A 858 Details of bonding type rmsd covalent geometry : bond 0.00291 (10723) covalent geometry : angle 0.60615 (14536) hydrogen bonds : bond 0.03581 ( 507) hydrogen bonds : angle 4.58553 ( 1389) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4200 (mmm) cc_final: 0.3801 (ppp) REVERT: A 513 LEU cc_start: 0.4322 (OUTLIER) cc_final: 0.3920 (pp) REVERT: B 955 PHE cc_start: 0.7654 (m-80) cc_final: 0.7267 (m-80) REVERT: B 1084 PHE cc_start: 0.3896 (OUTLIER) cc_final: 0.3242 (m-80) REVERT: B 1273 LEU cc_start: 0.8748 (tp) cc_final: 0.8475 (mm) REVERT: B 1275 GLN cc_start: 0.8258 (pp30) cc_final: 0.7787 (mp10) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.1124 time to fit residues: 17.2961 Evaluate side-chains 108 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain B residue 974 MET Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 111 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.194495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.137041 restraints weight = 14072.779| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.86 r_work: 0.3553 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10723 Z= 0.139 Angle : 0.616 14.354 14536 Z= 0.306 Chirality : 0.043 0.171 1603 Planarity : 0.004 0.040 1901 Dihedral : 4.781 57.717 1437 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 1.57 % Allowed : 15.38 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.50 (0.24), residues: 1312 helix: 1.15 (0.23), residues: 530 sheet: -0.47 (0.36), residues: 200 loop : 0.01 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1141 TYR 0.011 0.001 TYR B1002 PHE 0.014 0.001 PHE A 975 TRP 0.039 0.002 TRP B1145 HIS 0.003 0.001 HIS B1130 Details of bonding type rmsd covalent geometry : bond 0.00329 (10723) covalent geometry : angle 0.61640 (14536) hydrogen bonds : bond 0.03608 ( 507) hydrogen bonds : angle 4.55979 ( 1389) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4161 (mmm) cc_final: 0.3801 (ppp) REVERT: A 273 TYR cc_start: 0.7912 (m-80) cc_final: 0.7578 (m-80) REVERT: A 513 LEU cc_start: 0.4297 (OUTLIER) cc_final: 0.3885 (pp) REVERT: A 582 MET cc_start: 0.8773 (mmt) cc_final: 0.8546 (mmm) REVERT: B 1084 PHE cc_start: 0.3813 (OUTLIER) cc_final: 0.3155 (m-80) REVERT: B 1275 GLN cc_start: 0.8139 (pp30) cc_final: 0.7648 (mp10) outliers start: 18 outliers final: 15 residues processed: 108 average time/residue: 0.1093 time to fit residues: 16.9219 Evaluate side-chains 110 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain B residue 974 MET Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1084 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 12 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 97 optimal weight: 0.0060 chunk 60 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.194725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.136258 restraints weight = 14078.075| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.15 r_work: 0.3556 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10723 Z= 0.122 Angle : 0.618 13.975 14536 Z= 0.305 Chirality : 0.042 0.162 1603 Planarity : 0.004 0.040 1901 Dihedral : 4.658 55.242 1437 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 1.49 % Allowed : 15.47 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.61 (0.24), residues: 1312 helix: 1.26 (0.23), residues: 530 sheet: -0.35 (0.37), residues: 195 loop : 0.01 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.009 0.001 TYR B1002 PHE 0.013 0.001 PHE A 323 TRP 0.045 0.002 TRP B1145 HIS 0.003 0.001 HIS B1130 Details of bonding type rmsd covalent geometry : bond 0.00284 (10723) covalent geometry : angle 0.61759 (14536) hydrogen bonds : bond 0.03488 ( 507) hydrogen bonds : angle 4.56553 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3283.79 seconds wall clock time: 56 minutes 44.98 seconds (3404.98 seconds total)