Starting phenix.real_space_refine on Fri Sep 11 15:51:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bzf_30252/09_2026/7bzf_30252.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bzf_30252/09_2026/7bzf_30252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7bzf_30252/09_2026/7bzf_30252.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bzf_30252/09_2026/7bzf_30252.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bzf_30252/09_2026/7bzf_30252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bzf_30252/09_2026/7bzf_30252.map" model { file = "/net/cci-nas-00/data/ceres_data/7bzf_30252/09_2026/7bzf_30252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bzf_30252/09_2026/7bzf_30252.cif" } resolution = 3.26 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= 0.059 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 19 5.49 5 S 70 5.16 5 C 6245 2.51 5 N 1669 2.21 5 O 1927 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9932 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7333 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 883} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 519 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2450 SG CYS A 301 79.275 41.008 52.381 1.00 28.24 S ATOM 2523 SG CYS A 310 76.742 41.105 49.964 1.00 25.23 S ATOM 3925 SG CYS A 487 89.052 47.626 68.104 1.00 30.40 S ATOM 5178 SG CYS A 645 90.808 48.944 65.420 1.00 35.57 S ATOM 5184 SG CYS A 646 90.164 45.454 65.537 1.00 35.17 S Time building chain proxies: 2.07, per 1000 atoms: 0.21 Number of scatterers: 9932 At special positions: 0 Unit cell: (104.14, 103.32, 124.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 19 15.00 O 1927 8.00 N 1669 7.00 C 6245 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: 0.66 Conformation dependent library (CDL) restraints added in 246.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 3 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2302 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 43.8% alpha, 11.4% beta 9 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 removed outlier: 3.753A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.684A pdb=" N ALA A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.508A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.627A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 303 through 318 removed outlier: 4.070A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.645A pdb=" N ASP A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.785A pdb=" N ASP A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.598A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.346A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.812A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.640A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 708 removed outlier: 3.915A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.921A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 790 removed outlier: 4.126A pdb=" N SER A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 855 through 864 removed outlier: 3.899A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 896 removed outlier: 3.591A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 926 removed outlier: 3.924A pdb=" N TYR A 925 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.893A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.342A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.570A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.689A pdb=" N LEU B 180 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 4.047A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 94 Processing helix chain 'D' and resid 100 through 112 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.509A pdb=" N GLN A 57 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 66 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.505A pdb=" N ILE A 37 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.282A pdb=" N PHE A 102 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS A 113 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 111 " --> pdb=" O PHE A 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.527A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.570A pdb=" N VAL A 342 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 3.554A pdb=" N MET A 542 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR B 187 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA B 191 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N TRP B 154 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 612 through 616 removed outlier: 3.525A pdb=" N PHE A 766 " --> pdb=" O HIS A 613 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 754 " --> pdb=" O CYS A 765 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 612 through 616 removed outlier: 3.525A pdb=" N PHE A 766 " --> pdb=" O HIS A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AB1, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.597A pdb=" N THR D 187 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 142 through 143 379 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 0.91 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: 3113 1.34 - 1.46: 1710 1.46 - 1.57: 5220 1.57 - 1.69: 36 1.69 - 1.81: 105 Bond restraints: 10184 Sorted by residual: bond pdb=" C TRP B 182 " pdb=" N PRO B 183 " ideal model delta sigma weight residual 1.335 1.350 -0.015 8.70e-03 1.32e+04 3.10e+00 bond pdb=" CA SER A 709 " pdb=" C SER A 709 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.80e-02 3.09e+03 1.80e+00 bond pdb=" N ILE A 847 " pdb=" CA ILE A 847 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.33e+00 bond pdb=" CA VAL A 844 " pdb=" CB VAL A 844 " ideal model delta sigma weight residual 1.550 1.539 0.012 1.03e-02 9.43e+03 1.28e+00 bond pdb=" CA VAL D 167 " pdb=" CB VAL D 167 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.05e-02 9.07e+03 1.24e+00 ... (remaining 10179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 13683 2.10 - 4.19: 211 4.19 - 6.29: 20 6.29 - 8.38: 1 8.38 - 10.48: 1 Bond angle restraints: 13916 Sorted by residual: angle pdb=" C LEU A 119 " pdb=" N THR A 120 " pdb=" CA THR A 120 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C3' G F -3 " pdb=" O3' G F -3 " pdb=" P U F -2 " ideal model delta sigma weight residual 119.70 123.21 -3.51 1.20e+00 6.94e-01 8.58e+00 angle pdb=" C TYR A 787 " pdb=" N TYR A 788 " pdb=" CA TYR A 788 " ideal model delta sigma weight residual 122.26 117.24 5.02 1.73e+00 3.34e-01 8.43e+00 angle pdb=" C TRP A 916 " pdb=" N GLU A 917 " pdb=" CA GLU A 917 " ideal model delta sigma weight residual 121.95 132.43 -10.48 3.74e+00 7.15e-02 7.84e+00 angle pdb=" C ASP A 846 " pdb=" N ILE A 847 " pdb=" CA ILE A 847 " ideal model delta sigma weight residual 121.65 119.11 2.54 9.40e-01 1.13e+00 7.33e+00 ... (remaining 13911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.37: 5801 28.37 - 56.73: 212 56.73 - 85.10: 14 85.10 - 113.46: 2 113.46 - 141.83: 1 Dihedral angle restraints: 6030 sinusoidal: 2471 harmonic: 3559 Sorted by residual: dihedral pdb=" C4' U F 3 " pdb=" C3' U F 3 " pdb=" C2' U F 3 " pdb=" C1' U F 3 " ideal model delta sinusoidal sigma weight residual 36.35 -31.04 67.39 1 3.10e+00 1.04e-01 6.15e+02 dihedral pdb=" O4' U F 3 " pdb=" C4' U F 3 " pdb=" C3' U F 3 " pdb=" C2' U F 3 " ideal model delta sinusoidal sigma weight residual -35.15 21.29 -56.43 1 4.00e+00 6.25e-02 2.68e+02 dihedral pdb=" O4' U F 3 " pdb=" C2' U F 3 " pdb=" C1' U F 3 " pdb=" C3' U F 3 " ideal model delta sinusoidal sigma weight residual 25.59 -30.92 56.51 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 6027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1291 0.056 - 0.111: 262 0.111 - 0.167: 17 0.167 - 0.222: 8 0.222 - 0.278: 15 Chirality restraints: 1593 Sorted by residual: chirality pdb=" CB THR A 120 " pdb=" CA THR A 120 " pdb=" OG1 THR A 120 " pdb=" CG2 THR A 120 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C2' U F 3 " pdb=" C3' U F 3 " pdb=" O2' U F 3 " pdb=" C1' U F 3 " both_signs ideal model delta sigma weight residual False -2.79 -2.54 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" P U F -2 " pdb=" OP1 U F -2 " pdb=" OP2 U F -2 " pdb=" O5' U F -2 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1590 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO B 178 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " 0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO D 183 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G F -1 " -0.019 2.00e-02 2.50e+03 7.91e-03 1.88e+00 pdb=" N9 G F -1 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G F -1 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G F -1 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G F -1 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G F -1 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G F -1 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G F -1 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G F -1 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G F -1 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G F -1 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G F -1 " 0.003 2.00e-02 2.50e+03 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 964 2.74 - 3.28: 10318 3.28 - 3.82: 16222 3.82 - 4.36: 20084 4.36 - 4.90: 33800 Nonbonded interactions: 81388 Sorted by model distance: nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 294 " pdb=" OD1 ASN A 314 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP A 390 " pdb=" OH TYR A 674 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 433 " pdb=" O VAL A 435 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 420 " pdb=" OG SER C 4 " model vdw 2.259 3.040 ... (remaining 81383 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 84 through 122 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 188 or (resid 189 and (name N o \ r name CA or name C or name O or name CB )) or resid 190 through 191)) selection = (chain 'D' and (resid 84 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 191)) } 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: 2.140 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.800 Find NCS groups from input model: 0.180 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.692 10191 Z= 0.405 Angle : 0.743 28.251 13919 Z= 0.362 Chirality : 0.050 0.278 1593 Planarity : 0.003 0.039 1712 Dihedral : 14.343 141.826 3728 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -4.42 (0.19), residues: 1188 helix: -1.96 (0.19), residues: 500 sheet: -3.57 (0.36), residues: 133 loop : -3.74 (0.20), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.013 0.001 TYR A 921 PHE 0.015 0.001 PHE A 753 TRP 0.021 0.001 TRP D 182 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (10184) covalent geometry : angle 0.63006 / 0.35 (13916) hydrogen bonds : bond 0.12949 / 8.89 ( 399) hydrogen bonds : angle 6.20992 / 4.36 ( 1111) metal coordination : bond 0.43123 / 25.49 ( 7) metal coordination : angle 26.81661 / 14.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 452 ASP cc_start: 0.7776 (t70) cc_final: 0.7492 (t70) REVERT: D 106 ILE cc_start: 0.5964 (mm) cc_final: 0.5570 (mt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1176 time to fit residues: 26.7015 Evaluate side-chains 120 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 81 GLN A 113 HIS A 133 HIS A 312 ASN A 356 ASN A 439 HIS A 572 HIS A 650 HIS A 789 GLN B 108 ASN B 168 GLN C 36 HIS C 63 GLN D 104 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.160125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135895 restraints weight = 15915.677| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.46 r_work: 0.3643 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10191 Z= 0.142 Angle : 0.642 13.723 13919 Z= 0.319 Chirality : 0.048 0.559 1593 Planarity : 0.004 0.059 1712 Dihedral : 9.056 130.471 1530 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.14 % Allowed : 11.97 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.09 (0.22), residues: 1188 helix: -0.72 (0.22), residues: 491 sheet: -2.84 (0.40), residues: 129 loop : -3.14 (0.22), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 331 TYR 0.014 0.001 TYR A 887 PHE 0.016 0.001 PHE A 741 TRP 0.012 0.001 TRP D 182 HIS 0.007 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10184) covalent geometry : angle 0.63685 / 0.32 (13916) hydrogen bonds : bond 0.03776 / 2.53 ( 399) hydrogen bonds : angle 5.05384 / 3.58 ( 1111) metal coordination : bond 0.01384 / 0.83 ( 7) metal coordination : angle 5.76142 / 3.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 197 ARG cc_start: 0.5797 (tpp-160) cc_final: 0.5537 (tpp-160) REVERT: A 331 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.7229 (ttt-90) REVERT: A 452 ASP cc_start: 0.8477 (t70) cc_final: 0.8104 (t70) REVERT: A 500 LYS cc_start: 0.7577 (mmtt) cc_final: 0.7327 (mttm) REVERT: A 583 ARG cc_start: 0.8665 (mpt90) cc_final: 0.8394 (mmt180) REVERT: A 601 MET cc_start: 0.7645 (mtp) cc_final: 0.7442 (mtm) REVERT: A 818 MET cc_start: 0.8707 (ttp) cc_final: 0.8490 (ttt) REVERT: A 821 LYS cc_start: 0.8817 (tttm) cc_final: 0.8529 (tptp) REVERT: A 855 MET cc_start: 0.4945 (tpp) cc_final: 0.4539 (tpp) REVERT: A 919 GLU cc_start: 0.8074 (mp0) cc_final: 0.7785 (mp0) REVERT: D 94 MET cc_start: 0.6425 (mtt) cc_final: 0.6056 (mtp) REVERT: D 106 ILE cc_start: 0.5579 (mm) cc_final: 0.5227 (mt) outliers start: 12 outliers final: 8 residues processed: 145 average time/residue: 0.0965 time to fit residues: 19.8635 Evaluate side-chains 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 153 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.0010 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 HIS A 168 ASN C 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.160657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135978 restraints weight = 15965.187| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.48 r_work: 0.3651 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10191 Z= 0.138 Angle : 0.600 12.164 13919 Z= 0.301 Chirality : 0.047 0.546 1593 Planarity : 0.003 0.056 1712 Dihedral : 8.819 129.809 1530 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.90 % Allowed : 15.29 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -2.43 (0.23), residues: 1188 helix: -0.14 (0.23), residues: 487 sheet: -2.14 (0.44), residues: 122 loop : -2.89 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.014 0.001 TYR A 887 PHE 0.015 0.001 PHE A 741 TRP 0.011 0.001 TRP D 182 HIS 0.007 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10184) covalent geometry : angle 0.59675 / 0.30 (13916) hydrogen bonds : bond 0.03653 / 2.51 ( 399) hydrogen bonds : angle 4.80287 / 3.41 ( 1111) metal coordination : bond 0.00766 / 0.51 ( 7) metal coordination : angle 4.10902 / 2.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.372 Fit side-chains REVERT: A 102 PHE cc_start: 0.6665 (p90) cc_final: 0.6146 (p90) REVERT: A 160 LYS cc_start: 0.7746 (tppt) cc_final: 0.7134 (ptmt) REVERT: A 197 ARG cc_start: 0.5665 (tpp-160) cc_final: 0.5379 (tpp-160) REVERT: A 331 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.7172 (ttt-90) REVERT: A 340 PHE cc_start: 0.8715 (m-80) cc_final: 0.8509 (m-10) REVERT: A 452 ASP cc_start: 0.8418 (t70) cc_final: 0.8031 (t70) REVERT: A 500 LYS cc_start: 0.7512 (mmtt) cc_final: 0.7307 (mttm) REVERT: A 583 ARG cc_start: 0.8647 (mpt90) cc_final: 0.8333 (mmt180) REVERT: A 919 GLU cc_start: 0.8021 (mp0) cc_final: 0.7636 (mp0) REVERT: D 87 MET cc_start: 0.5477 (tpp) cc_final: 0.5268 (tpp) REVERT: D 94 MET cc_start: 0.6297 (mtt) cc_final: 0.5984 (mtp) REVERT: D 106 ILE cc_start: 0.5442 (mm) cc_final: 0.5089 (mt) outliers start: 20 outliers final: 13 residues processed: 144 average time/residue: 0.1037 time to fit residues: 21.1231 Evaluate side-chains 137 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 1 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 HIS A 168 ASN A 752 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.139254 restraints weight = 15998.961| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.50 r_work: 0.3679 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10191 Z= 0.106 Angle : 0.565 11.639 13919 Z= 0.283 Chirality : 0.046 0.490 1593 Planarity : 0.003 0.047 1712 Dihedral : 8.689 131.421 1530 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.71 % Allowed : 16.24 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.93 (0.24), residues: 1188 helix: 0.19 (0.24), residues: 491 sheet: -1.86 (0.46), residues: 122 loop : -2.54 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.014 0.001 TYR A 887 PHE 0.015 0.001 PHE A 741 TRP 0.009 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (10184) covalent geometry : angle 0.56316 / 0.28 (13916) hydrogen bonds : bond 0.03201 / 2.16 ( 399) hydrogen bonds : angle 4.57969 / 3.25 ( 1111) metal coordination : bond 0.00500 / 0.35 ( 7) metal coordination : angle 3.07144 / 1.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.364 Fit side-chains REVERT: A 197 ARG cc_start: 0.5553 (tpp-160) cc_final: 0.5275 (tpp-160) REVERT: A 391 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8173 (mmtm) REVERT: A 452 ASP cc_start: 0.8355 (t70) cc_final: 0.7978 (t70) REVERT: A 552 ASN cc_start: 0.7625 (p0) cc_final: 0.7074 (t0) REVERT: A 583 ARG cc_start: 0.8619 (mpt90) cc_final: 0.8330 (mmt180) REVERT: A 608 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: A 821 LYS cc_start: 0.8874 (tttm) cc_final: 0.8663 (tptp) REVERT: A 880 VAL cc_start: 0.8124 (t) cc_final: 0.7839 (t) REVERT: A 919 GLU cc_start: 0.8008 (mp0) cc_final: 0.7582 (mp0) REVERT: B 96 ARG cc_start: 0.7673 (mmp80) cc_final: 0.7457 (tpm170) REVERT: D 94 MET cc_start: 0.6387 (mtt) cc_final: 0.6100 (mtp) REVERT: D 106 ILE cc_start: 0.5539 (mm) cc_final: 0.5168 (mt) REVERT: D 117 LEU cc_start: 0.7303 (mm) cc_final: 0.7098 (mm) outliers start: 18 outliers final: 12 residues processed: 141 average time/residue: 0.0983 time to fit residues: 19.7580 Evaluate side-chains 134 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 101 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 118 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 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 = 0.4059 r_free = 0.4059 target = 0.162567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137874 restraints weight = 15886.736| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.49 r_work: 0.3674 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10191 Z= 0.129 Angle : 0.579 10.948 13919 Z= 0.288 Chirality : 0.046 0.440 1593 Planarity : 0.003 0.045 1712 Dihedral : 8.643 128.594 1530 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.09 % Allowed : 16.81 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.72 (0.24), residues: 1188 helix: 0.43 (0.24), residues: 480 sheet: -2.01 (0.45), residues: 128 loop : -2.37 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.013 0.001 TYR A 887 PHE 0.014 0.001 PHE A 741 TRP 0.008 0.001 TRP D 182 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10184) covalent geometry : angle 0.57683 / 0.29 (13916) hydrogen bonds : bond 0.03367 / 2.29 ( 399) hydrogen bonds : angle 4.55694 / 3.25 ( 1111) metal coordination : bond 0.00604 / 0.40 ( 7) metal coordination : angle 3.05643 / 1.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.308 Fit side-chains REVERT: A 102 PHE cc_start: 0.6427 (p90) cc_final: 0.5976 (p90) REVERT: A 144 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 197 ARG cc_start: 0.5555 (tpp-160) cc_final: 0.5282 (tpp-160) REVERT: A 340 PHE cc_start: 0.8716 (m-10) cc_final: 0.8495 (m-10) REVERT: A 452 ASP cc_start: 0.8329 (t70) cc_final: 0.7944 (t70) REVERT: A 546 TYR cc_start: 0.6690 (t80) cc_final: 0.6242 (t80) REVERT: A 608 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: A 665 GLU cc_start: 0.8291 (pm20) cc_final: 0.7124 (pm20) REVERT: A 821 LYS cc_start: 0.8888 (tttm) cc_final: 0.8580 (tptp) REVERT: A 880 VAL cc_start: 0.8122 (t) cc_final: 0.7841 (t) REVERT: A 919 GLU cc_start: 0.8022 (mp0) cc_final: 0.7578 (mp0) REVERT: B 96 ARG cc_start: 0.7698 (mmp80) cc_final: 0.7495 (mmt180) REVERT: D 94 MET cc_start: 0.6306 (mtt) cc_final: 0.6042 (mtp) outliers start: 22 outliers final: 15 residues processed: 137 average time/residue: 0.1070 time to fit residues: 20.5693 Evaluate side-chains 135 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 99 optimal weight: 0.1980 chunk 115 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 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 = 0.4075 r_free = 0.4075 target = 0.164110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.139315 restraints weight = 15977.759| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.52 r_work: 0.3689 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10191 Z= 0.112 Angle : 0.565 10.529 13919 Z= 0.281 Chirality : 0.045 0.391 1593 Planarity : 0.003 0.040 1712 Dihedral : 8.664 130.966 1530 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.09 % Allowed : 16.81 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.58 (0.24), residues: 1188 helix: 0.44 (0.24), residues: 491 sheet: -1.66 (0.47), residues: 122 loop : -2.31 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.013 0.001 TYR A 887 PHE 0.014 0.001 PHE A 741 TRP 0.007 0.001 TRP D 182 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10184) covalent geometry : angle 0.56391 / 0.28 (13916) hydrogen bonds : bond 0.03147 / 2.13 ( 399) hydrogen bonds : angle 4.46762 / 3.17 ( 1111) metal coordination : bond 0.00456 / 0.30 ( 7) metal coordination : angle 2.63615 / 1.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.361 Fit side-chains REVERT: A 102 PHE cc_start: 0.6354 (p90) cc_final: 0.5922 (p90) REVERT: A 340 PHE cc_start: 0.8713 (m-10) cc_final: 0.8481 (m-10) REVERT: A 391 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8165 (mmtm) REVERT: A 452 ASP cc_start: 0.8324 (t70) cc_final: 0.7944 (t70) REVERT: A 546 TYR cc_start: 0.6852 (t80) cc_final: 0.6463 (t80) REVERT: A 665 GLU cc_start: 0.8267 (pm20) cc_final: 0.7087 (pm20) REVERT: A 805 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7172 (tp) REVERT: A 821 LYS cc_start: 0.8843 (tttm) cc_final: 0.8532 (tptp) REVERT: A 919 GLU cc_start: 0.7970 (mp0) cc_final: 0.7534 (mp0) REVERT: B 96 ARG cc_start: 0.7670 (mmp80) cc_final: 0.7425 (mmt180) REVERT: C 3 MET cc_start: 0.6608 (mmm) cc_final: 0.5891 (tpt) REVERT: D 94 MET cc_start: 0.6302 (mtt) cc_final: 0.6089 (mtp) outliers start: 22 outliers final: 15 residues processed: 144 average time/residue: 0.0965 time to fit residues: 20.0554 Evaluate side-chains 138 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS A 573 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.160904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136063 restraints weight = 15975.225| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.49 r_work: 0.3644 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10191 Z= 0.156 Angle : 0.608 9.766 13919 Z= 0.302 Chirality : 0.046 0.343 1593 Planarity : 0.003 0.038 1712 Dihedral : 8.660 127.937 1530 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.28 % Allowed : 17.47 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.57 (0.24), residues: 1188 helix: 0.48 (0.24), residues: 480 sheet: -1.78 (0.46), residues: 128 loop : -2.24 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.017 0.002 TYR A 286 PHE 0.014 0.001 PHE A 741 TRP 0.009 0.001 TRP B 154 HIS 0.003 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (10184) covalent geometry : angle 0.60635 / 0.30 (13916) hydrogen bonds : bond 0.03598 / 2.48 ( 399) hydrogen bonds : angle 4.56195 / 3.23 ( 1111) metal coordination : bond 0.00763 / 0.50 ( 7) metal coordination : angle 3.08713 / 1.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.407 Fit side-chains REVERT: A 102 PHE cc_start: 0.6493 (p90) cc_final: 0.6040 (p90) REVERT: A 144 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7276 (mt-10) REVERT: A 340 PHE cc_start: 0.8801 (m-10) cc_final: 0.8545 (m-10) REVERT: A 452 ASP cc_start: 0.8311 (t70) cc_final: 0.7931 (t70) REVERT: A 665 GLU cc_start: 0.8295 (pm20) cc_final: 0.7155 (pm20) REVERT: A 821 LYS cc_start: 0.8871 (tttm) cc_final: 0.8542 (tptp) REVERT: A 880 VAL cc_start: 0.8028 (t) cc_final: 0.7791 (t) REVERT: A 919 GLU cc_start: 0.7968 (mp0) cc_final: 0.7547 (mp0) REVERT: B 80 ARG cc_start: 0.7994 (mtp-110) cc_final: 0.7656 (ttm170) REVERT: C 3 MET cc_start: 0.6509 (mmm) cc_final: 0.5857 (tpt) outliers start: 24 outliers final: 21 residues processed: 138 average time/residue: 0.1040 time to fit residues: 20.5140 Evaluate side-chains 143 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 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 = 0.4079 r_free = 0.4079 target = 0.164285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139487 restraints weight = 15832.853| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.51 r_work: 0.3675 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10191 Z= 0.109 Angle : 0.573 9.641 13919 Z= 0.283 Chirality : 0.045 0.324 1593 Planarity : 0.003 0.034 1712 Dihedral : 8.621 132.623 1530 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.90 % Allowed : 18.52 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.46 (0.24), residues: 1188 helix: 0.51 (0.24), residues: 491 sheet: -1.86 (0.44), residues: 137 loop : -2.13 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 631 TYR 0.013 0.001 TYR A 286 PHE 0.014 0.001 PHE A 741 TRP 0.008 0.001 TRP C 29 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10184) covalent geometry : angle 0.57213 / 0.28 (13916) hydrogen bonds : bond 0.03129 / 2.12 ( 399) hydrogen bonds : angle 4.44668 / 3.15 ( 1111) metal coordination : bond 0.00398 / 0.26 ( 7) metal coordination : angle 2.48153 / 1.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.377 Fit side-chains REVERT: A 102 PHE cc_start: 0.6282 (p90) cc_final: 0.5831 (p90) REVERT: A 144 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7191 (mt-10) REVERT: A 340 PHE cc_start: 0.8754 (m-10) cc_final: 0.8512 (m-10) REVERT: A 391 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8164 (mmtm) REVERT: A 418 ASP cc_start: 0.7414 (t0) cc_final: 0.6954 (t70) REVERT: A 452 ASP cc_start: 0.8318 (t70) cc_final: 0.7917 (t70) REVERT: A 665 GLU cc_start: 0.8244 (pm20) cc_final: 0.7085 (pm20) REVERT: A 805 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7077 (tp) REVERT: A 821 LYS cc_start: 0.8820 (tttm) cc_final: 0.8438 (tptp) REVERT: A 880 VAL cc_start: 0.7908 (t) cc_final: 0.7660 (t) REVERT: A 919 GLU cc_start: 0.7917 (mp0) cc_final: 0.7465 (mp0) REVERT: B 80 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7644 (ttm170) outliers start: 20 outliers final: 17 residues processed: 147 average time/residue: 0.1108 time to fit residues: 22.8273 Evaluate side-chains 144 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 42 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 5 optimal weight: 10.0000 chunk 108 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.165529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140582 restraints weight = 15915.312| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.52 r_work: 0.3697 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10191 Z= 0.107 Angle : 0.571 9.267 13919 Z= 0.281 Chirality : 0.044 0.322 1593 Planarity : 0.003 0.034 1712 Dihedral : 8.566 132.617 1530 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.52 % Allowed : 18.90 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.32 (0.24), residues: 1188 helix: 0.62 (0.24), residues: 490 sheet: -1.75 (0.44), residues: 137 loop : -2.05 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 836 TYR 0.012 0.001 TYR A 286 PHE 0.016 0.001 PHE A 753 TRP 0.008 0.001 TRP C 29 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10184) covalent geometry : angle 0.57029 / 0.28 (13916) hydrogen bonds : bond 0.03056 / 2.06 ( 399) hydrogen bonds : angle 4.40309 / 3.11 ( 1111) metal coordination : bond 0.00377 / 0.25 ( 7) metal coordination : angle 2.30672 / 1.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.375 Fit side-chains REVERT: A 102 PHE cc_start: 0.6069 (p90) cc_final: 0.5667 (p90) REVERT: A 144 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7145 (mt-10) REVERT: A 340 PHE cc_start: 0.8793 (m-10) cc_final: 0.8567 (m-10) REVERT: A 391 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8141 (mmtm) REVERT: A 418 ASP cc_start: 0.7432 (t0) cc_final: 0.6970 (t70) REVERT: A 452 ASP cc_start: 0.8267 (t70) cc_final: 0.7861 (t70) REVERT: A 665 GLU cc_start: 0.8217 (pm20) cc_final: 0.7111 (pm20) REVERT: A 805 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7111 (tp) REVERT: A 821 LYS cc_start: 0.8798 (tttm) cc_final: 0.8426 (tptp) REVERT: A 880 VAL cc_start: 0.7922 (t) cc_final: 0.7699 (t) REVERT: A 919 GLU cc_start: 0.7933 (mp0) cc_final: 0.7497 (mp0) REVERT: B 80 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7654 (ttm170) REVERT: B 96 ARG cc_start: 0.7646 (mmp80) cc_final: 0.7338 (mmt180) outliers start: 16 outliers final: 15 residues processed: 146 average time/residue: 0.1056 time to fit residues: 21.7357 Evaluate side-chains 148 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 109 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 106 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.163862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138779 restraints weight = 15687.019| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.53 r_work: 0.3680 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10191 Z= 0.113 Angle : 0.582 9.959 13919 Z= 0.287 Chirality : 0.044 0.324 1593 Planarity : 0.003 0.034 1712 Dihedral : 8.542 132.534 1530 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.99 % Allowed : 18.80 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.21 (0.24), residues: 1188 helix: 0.73 (0.24), residues: 484 sheet: -1.58 (0.45), residues: 132 loop : -2.02 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 836 TYR 0.015 0.001 TYR A 286 PHE 0.015 0.001 PHE A 741 TRP 0.008 0.001 TRP A 617 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10184) covalent geometry : angle 0.58065 / 0.29 (13916) hydrogen bonds : bond 0.03076 / 2.09 ( 399) hydrogen bonds : angle 4.37450 / 3.08 ( 1111) metal coordination : bond 0.00412 / 0.26 ( 7) metal coordination : angle 2.34379 / 1.36 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.424 Fit side-chains REVERT: A 102 PHE cc_start: 0.6076 (p90) cc_final: 0.5701 (p90) REVERT: A 144 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7128 (mt-10) REVERT: A 160 LYS cc_start: 0.7776 (tppt) cc_final: 0.6692 (ttpt) REVERT: A 340 PHE cc_start: 0.8806 (m-10) cc_final: 0.8587 (m-10) REVERT: A 391 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8197 (mmtm) REVERT: A 418 ASP cc_start: 0.7480 (t0) cc_final: 0.7038 (t70) REVERT: A 452 ASP cc_start: 0.8269 (t70) cc_final: 0.7888 (t70) REVERT: A 665 GLU cc_start: 0.8212 (pm20) cc_final: 0.7204 (pm20) REVERT: A 805 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7034 (tp) REVERT: A 821 LYS cc_start: 0.8793 (tttm) cc_final: 0.8443 (tptp) REVERT: A 919 GLU cc_start: 0.7926 (mp0) cc_final: 0.7510 (mp0) REVERT: B 80 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.7609 (ttm170) REVERT: B 96 ARG cc_start: 0.7728 (mmp80) cc_final: 0.7418 (mmt180) outliers start: 21 outliers final: 16 residues processed: 143 average time/residue: 0.1055 time to fit residues: 21.2961 Evaluate side-chains 146 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.0670 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 117 optimal weight: 0.0370 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.164847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.139545 restraints weight = 15884.650| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.56 r_work: 0.3692 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10191 Z= 0.107 Angle : 0.572 8.692 13919 Z= 0.283 Chirality : 0.044 0.319 1593 Planarity : 0.003 0.034 1712 Dihedral : 8.491 133.543 1530 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.71 % Allowed : 18.80 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.16 (0.24), residues: 1188 helix: 0.76 (0.24), residues: 490 sheet: -1.56 (0.45), residues: 132 loop : -1.99 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 836 TYR 0.013 0.001 TYR A 286 PHE 0.015 0.001 PHE A 741 TRP 0.008 0.001 TRP C 29 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (10184) covalent geometry : angle 0.57154 / 0.28 (13916) hydrogen bonds : bond 0.02946 / 1.98 ( 399) hydrogen bonds : angle 4.31173 / 3.04 ( 1111) metal coordination : bond 0.00365 / 0.24 ( 7) metal coordination : angle 2.20536 / 1.27 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2175.13 seconds wall clock time: 38 minutes 11.59 seconds (2291.59 seconds total)