Starting phenix.real_space_refine on Fri Jun 13 13:21:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dde_46771/06_2025/9dde_46771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dde_46771/06_2025/9dde_46771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dde_46771/06_2025/9dde_46771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dde_46771/06_2025/9dde_46771.map" model { file = "/net/cci-nas-00/data/ceres_data/9dde_46771/06_2025/9dde_46771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dde_46771/06_2025/9dde_46771.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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 5 6.06 5 P 324 5.49 5 S 34 5.16 5 C 8654 2.51 5 N 2852 2.21 5 O 3525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15394 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 663 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3345 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "J" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3297 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "K" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 783 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 93} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 467 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "O" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 467 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 69} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "K" 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} Chain: "L" 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} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12728 SG CYS K 18 110.369 47.497 86.380 1.00172.81 S ATOM 12749 SG CYS K 21 113.957 46.507 85.515 1.00171.27 S ATOM 12887 SG CYS K 39 112.069 48.574 83.128 1.00170.07 S ATOM 12909 SG CYS K 42 111.045 44.883 83.675 1.00170.96 S ATOM 12846 SG CYS K 34 98.527 51.073 90.704 1.00173.73 S ATOM 12996 SG CYS K 53 100.863 48.206 91.830 1.00177.96 S ATOM 13017 SG CYS K 56 98.621 49.902 94.368 1.00184.67 S ATOM 13653 SG CYS L 51 100.265 74.273 84.400 1.00185.19 S ATOM 13674 SG CYS L 54 101.442 77.195 86.194 1.00181.49 S ATOM 13815 SG CYS L 72 100.667 73.995 88.092 1.00169.07 S ATOM 13834 SG CYS L 75 97.777 76.217 86.748 1.00168.71 S ATOM 13769 SG CYS L 67 94.926 63.191 78.331 1.00151.96 S ATOM 13923 SG CYS L 87 95.103 66.989 77.587 1.00170.12 S ATOM 13943 SG CYS L 90 95.202 64.478 74.680 1.00157.27 S ATOM 14193 SG CYS M 27 29.418 51.535 66.943 1.00123.52 S ATOM 14212 SG CYS M 30 27.721 52.692 63.677 1.00112.94 S ATOM 14292 SG CYS M 41 29.720 49.538 63.755 1.00100.03 S ATOM 14312 SG CYS M 44 31.513 52.805 63.995 1.00 94.27 S Time building chain proxies: 9.93, per 1000 atoms: 0.65 Number of scatterers: 15394 At special positions: 0 Unit cell: (137.541, 124.545, 144.039, 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 5 29.99 S 34 16.00 P 324 15.00 O 3525 8.00 N 2852 7.00 C 8654 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: 3.87 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 21 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 18 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 42 " pdb=" ZN K 402 " pdb="ZN ZN K 402 " - pdb=" ND1 HIS K 36 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 56 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 34 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 72 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 75 " pdb=" ZN L 402 " pdb="ZN ZN L 402 " - pdb=" ND1 HIS L 69 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 90 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 87 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 67 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 41 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 44 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 30 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 27 " Number of angles added : 24 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 60.5% alpha, 5.8% beta 161 base pairs and 290 stacking pairs defined. Time for finding SS restraints: 12.57 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.503A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.892A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.645A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.175A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.632A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.502A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 9 through 13 Processing helix chain 'K' and resid 14 through 16 No H-bonds generated for 'chain 'K' and resid 14 through 16' Processing helix chain 'K' and resid 40 through 48 Processing helix chain 'K' and resid 64 through 67 Processing helix chain 'K' and resid 72 through 83 Processing helix chain 'K' and resid 85 through 99 Processing helix chain 'L' and resid 45 through 50 Processing helix chain 'L' and resid 73 through 83 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'L' and resid 103 through 114 Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'O' and resid 38 through 51 removed outlier: 4.345A pdb=" N LEU O 42 " --> pdb=" O PRO O 38 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER O 50 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS O 51 " --> pdb=" O VAL O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 69 Processing helix chain 'O' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.482A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.852A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.861A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.295A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'K' and resid 36 through 39 Processing sheet with id=AB4, first strand: chain 'L' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB6, first strand: chain 'N' and resid 12 through 16 removed outlier: 9.330A pdb=" N LEU N 67 " --> pdb=" O GLN N 2 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU N 69 " --> pdb=" O PHE N 4 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 56 through 57 523 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 415 hydrogen bonds 830 hydrogen bond angles 0 basepair planarities 161 basepair parallelities 290 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3440 1.33 - 1.46: 4869 1.46 - 1.58: 7316 1.58 - 1.70: 646 1.70 - 1.82: 46 Bond restraints: 16317 Sorted by residual: bond pdb=" N GLY M 49 " pdb=" CA GLY M 49 " ideal model delta sigma weight residual 1.444 1.477 -0.033 9.60e-03 1.09e+04 1.18e+01 bond pdb=" N ASN K 13 " pdb=" CA ASN K 13 " ideal model delta sigma weight residual 1.462 1.494 -0.032 9.50e-03 1.11e+04 1.15e+01 bond pdb=" N ILE B 29 " pdb=" CA ILE B 29 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.08e-02 8.57e+03 9.51e+00 bond pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.95e+00 bond pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 1.462 1.487 -0.026 9.50e-03 1.11e+04 7.36e+00 ... (remaining 16312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 22940 1.91 - 3.81: 484 3.81 - 5.72: 42 5.72 - 7.63: 15 7.63 - 9.54: 1 Bond angle restraints: 23482 Sorted by residual: angle pdb=" CB LYS K 81 " pdb=" CG LYS K 81 " pdb=" CD LYS K 81 " ideal model delta sigma weight residual 111.30 120.84 -9.54 2.30e+00 1.89e-01 1.72e+01 angle pdb=" N ASN B 25 " pdb=" CA ASN B 25 " pdb=" C ASN B 25 " ideal model delta sigma weight residual 114.12 108.81 5.31 1.39e+00 5.18e-01 1.46e+01 angle pdb=" N ASP G 72 " pdb=" CA ASP G 72 " pdb=" C ASP G 72 " ideal model delta sigma weight residual 112.54 108.51 4.03 1.22e+00 6.72e-01 1.09e+01 angle pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" C ASN F 25 " ideal model delta sigma weight residual 113.23 109.20 4.03 1.24e+00 6.50e-01 1.06e+01 angle pdb=" CA ASP B 24 " pdb=" C ASP B 24 " pdb=" O ASP B 24 " ideal model delta sigma weight residual 122.03 118.12 3.91 1.25e+00 6.40e-01 9.81e+00 ... (remaining 23477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.75: 6847 26.75 - 53.50: 1840 53.50 - 80.25: 274 80.25 - 107.00: 3 107.00 - 133.76: 2 Dihedral angle restraints: 8966 sinusoidal: 5630 harmonic: 3336 Sorted by residual: dihedral pdb=" C4' DC I 36 " pdb=" C3' DC I 36 " pdb=" O3' DC I 36 " pdb=" P DT I 37 " ideal model delta sinusoidal sigma weight residual 220.00 86.24 133.76 1 3.50e+01 8.16e-04 1.33e+01 dihedral pdb=" CA LYS K 8 " pdb=" C LYS K 8 " pdb=" N ILE K 9 " pdb=" CA ILE K 9 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" C4' DC I 128 " pdb=" C3' DC I 128 " pdb=" O3' DC I 128 " pdb=" P DT I 129 " ideal model delta sinusoidal sigma weight residual 220.00 91.73 128.27 1 3.50e+01 8.16e-04 1.27e+01 ... (remaining 8963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2694 0.109 - 0.218: 27 0.218 - 0.326: 1 0.326 - 0.435: 0 0.435 - 0.544: 6 Chirality restraints: 2728 Sorted by residual: chirality pdb=" P DC I 173 " pdb=" OP1 DC I 173 " pdb=" OP2 DC I 173 " pdb=" O5' DC I 173 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" P DA J 151 " pdb=" OP1 DA J 151 " pdb=" OP2 DA J 151 " pdb=" O5' DA J 151 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.97e+00 chirality pdb=" P DG I 174 " pdb=" OP1 DG I 174 " pdb=" OP2 DG I 174 " pdb=" O5' DG I 174 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.62e+00 ... (remaining 2725 not shown) Planarity restraints: 1851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 48 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C ASP D 48 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP D 48 " -0.018 2.00e-02 2.50e+03 pdb=" N THR D 49 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " 0.019 2.00e-02 2.50e+03 1.61e-02 5.16e+00 pdb=" CG TYR D 80 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 23 " 0.193 9.50e-02 1.11e+02 8.64e-02 4.59e+00 pdb=" NE ARG B 23 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 23 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 23 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 23 " 0.007 2.00e-02 2.50e+03 ... (remaining 1848 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2156 2.76 - 3.30: 13224 3.30 - 3.83: 28260 3.83 - 4.37: 32748 4.37 - 4.90: 48324 Nonbonded interactions: 124712 Sorted by model distance: nonbonded pdb=" OE2 GLU O 52 " pdb=" OG SER O 54 " model vdw 2.226 3.040 nonbonded pdb=" N GLN L 25 " pdb=" OE1 GLN L 25 " model vdw 2.229 3.120 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.239 3.040 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.248 3.120 nonbonded pdb=" O LEU L 80 " pdb=" NZ LYS L 85 " model vdw 2.297 3.120 ... (remaining 124707 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 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 53.600 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.004 0.056 16337 Z= 0.225 Angle : 0.654 9.537 23506 Z= 0.394 Chirality : 0.044 0.544 2728 Planarity : 0.005 0.086 1851 Dihedral : 26.365 133.756 6802 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.33 % Allowed : 14.32 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.25), residues: 1121 helix: 2.48 (0.20), residues: 658 sheet: 0.20 (0.85), residues: 35 loop : -0.86 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 25 HIS 0.009 0.001 HIS C 31 PHE 0.013 0.001 PHE E 78 TYR 0.038 0.002 TYR D 80 ARG 0.009 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.06812 ( 938) hydrogen bonds : angle 3.32878 ( 2360) metal coordination : bond 0.01036 ( 20) metal coordination : angle 2.63993 ( 24) covalent geometry : bond 0.00439 (16317) covalent geometry : angle 0.64878 (23482) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 307 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8917 (tttp) cc_final: 0.8701 (ttmm) REVERT: F 67 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8132 (ttm-80) REVERT: K 70 ARG cc_start: 0.8713 (mmt90) cc_final: 0.8464 (mmt-90) REVERT: K 74 THR cc_start: 0.8779 (p) cc_final: 0.8491 (t) REVERT: K 80 TYR cc_start: 0.8022 (m-80) cc_final: 0.7786 (m-10) REVERT: K 90 GLU cc_start: 0.9083 (tp30) cc_final: 0.8862 (tp30) REVERT: L 61 THR cc_start: 0.9312 (m) cc_final: 0.9015 (p) REVERT: L 71 PHE cc_start: 0.8741 (m-80) cc_final: 0.8198 (m-80) REVERT: M 61 LEU cc_start: 0.7939 (tp) cc_final: 0.7280 (pt) outliers start: 3 outliers final: 0 residues processed: 308 average time/residue: 0.3592 time to fit residues: 150.5189 Evaluate side-chains 247 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 43 optimal weight: 0.0050 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 HIS H 46 HIS K 76 GLN N 68 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.054123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.033037 restraints weight = 79119.286| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 3.57 r_work: 0.2447 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 16337 Z= 0.385 Angle : 0.686 10.070 23506 Z= 0.396 Chirality : 0.042 0.140 2728 Planarity : 0.005 0.049 1851 Dihedral : 29.104 122.985 4782 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.33 % Allowed : 16.87 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.25), residues: 1121 helix: 2.39 (0.20), residues: 662 sheet: 0.04 (0.88), residues: 35 loop : -0.91 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 25 HIS 0.004 0.001 HIS C 31 PHE 0.017 0.002 PHE M 24 TYR 0.062 0.002 TYR D 80 ARG 0.007 0.001 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.06756 ( 938) hydrogen bonds : angle 3.50334 ( 2360) metal coordination : bond 0.02443 ( 20) metal coordination : angle 3.38311 ( 24) covalent geometry : bond 0.00872 (16317) covalent geometry : angle 0.67730 (23482) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.9208 (t0) cc_final: 0.8954 (t0) REVERT: E 59 GLU cc_start: 0.8960 (pm20) cc_final: 0.8707 (pm20) REVERT: G 17 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8831 (mtm180) REVERT: H 31 LYS cc_start: 0.9512 (mttt) cc_final: 0.9277 (mptt) REVERT: H 73 GLU cc_start: 0.9312 (tp30) cc_final: 0.8784 (tp30) REVERT: K 45 ARG cc_start: 0.9735 (mmt90) cc_final: 0.9310 (mmp80) REVERT: K 74 THR cc_start: 0.7438 (p) cc_final: 0.7222 (t) REVERT: L 61 THR cc_start: 0.8832 (m) cc_final: 0.8429 (p) REVERT: M 61 LEU cc_start: 0.8605 (tp) cc_final: 0.8161 (pt) outliers start: 30 outliers final: 20 residues processed: 251 average time/residue: 0.3276 time to fit residues: 113.1232 Evaluate side-chains 243 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain N residue 8 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 62 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.054602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.033602 restraints weight = 78723.267| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 3.58 r_work: 0.2479 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16337 Z= 0.254 Angle : 0.601 7.851 23506 Z= 0.351 Chirality : 0.037 0.155 2728 Planarity : 0.004 0.040 1851 Dihedral : 28.897 121.187 4782 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.44 % Allowed : 19.20 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.25), residues: 1121 helix: 2.59 (0.20), residues: 662 sheet: -0.06 (0.87), residues: 35 loop : -0.86 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP M 25 HIS 0.003 0.001 HIS F 75 PHE 0.013 0.002 PHE E 78 TYR 0.046 0.002 TYR D 80 ARG 0.005 0.001 ARG L 70 Details of bonding type rmsd hydrogen bonds : bond 0.05274 ( 938) hydrogen bonds : angle 3.18096 ( 2360) metal coordination : bond 0.01486 ( 20) metal coordination : angle 3.59810 ( 24) covalent geometry : bond 0.00568 (16317) covalent geometry : angle 0.59020 (23482) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9252 (tp30) cc_final: 0.8868 (tp30) REVERT: C 90 ASP cc_start: 0.9130 (t0) cc_final: 0.8721 (t0) REVERT: E 59 GLU cc_start: 0.8883 (pm20) cc_final: 0.8641 (pm20) REVERT: G 17 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8793 (mtt180) REVERT: H 31 LYS cc_start: 0.9477 (mttt) cc_final: 0.9260 (mptt) REVERT: K 74 THR cc_start: 0.7364 (p) cc_final: 0.7139 (t) REVERT: M 47 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8531 (mmm-85) REVERT: M 61 LEU cc_start: 0.8688 (tp) cc_final: 0.8260 (pt) outliers start: 22 outliers final: 13 residues processed: 238 average time/residue: 0.3385 time to fit residues: 111.0878 Evaluate side-chains 240 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 133 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 138 optimal weight: 0.0060 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.054838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.034178 restraints weight = 79782.849| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.59 r_work: 0.2505 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16337 Z= 0.207 Angle : 0.576 8.354 23506 Z= 0.337 Chirality : 0.036 0.148 2728 Planarity : 0.004 0.039 1851 Dihedral : 28.720 120.949 4782 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.11 % Allowed : 18.98 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.25), residues: 1121 helix: 2.65 (0.20), residues: 664 sheet: -0.33 (0.89), residues: 35 loop : -0.81 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP M 25 HIS 0.003 0.001 HIS K 61 PHE 0.017 0.002 PHE K 38 TYR 0.016 0.001 TYR D 80 ARG 0.006 0.001 ARG K 45 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 938) hydrogen bonds : angle 3.03837 ( 2360) metal coordination : bond 0.01165 ( 20) metal coordination : angle 3.15575 ( 24) covalent geometry : bond 0.00459 (16317) covalent geometry : angle 0.56746 (23482) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9265 (tp30) cc_final: 0.8695 (tp30) REVERT: B 63 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8687 (mt-10) REVERT: C 90 ASP cc_start: 0.8997 (t0) cc_final: 0.8792 (t0) REVERT: E 59 GLU cc_start: 0.8829 (pm20) cc_final: 0.8578 (pm20) REVERT: K 74 THR cc_start: 0.7395 (p) cc_final: 0.7165 (t) REVERT: M 61 LEU cc_start: 0.8819 (tp) cc_final: 0.8393 (pt) outliers start: 28 outliers final: 18 residues processed: 252 average time/residue: 0.3127 time to fit residues: 110.4707 Evaluate side-chains 245 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 106 PHE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.055622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.034960 restraints weight = 79693.015| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.51 r_work: 0.2548 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16337 Z= 0.160 Angle : 0.558 8.711 23506 Z= 0.325 Chirality : 0.034 0.152 2728 Planarity : 0.004 0.037 1851 Dihedral : 28.564 120.031 4782 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.44 % Allowed : 20.64 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.26), residues: 1121 helix: 2.72 (0.20), residues: 668 sheet: -0.35 (0.89), residues: 36 loop : -0.68 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP M 25 HIS 0.002 0.000 HIS B 75 PHE 0.011 0.001 PHE K 38 TYR 0.014 0.001 TYR D 80 ARG 0.005 0.001 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 938) hydrogen bonds : angle 2.89011 ( 2360) metal coordination : bond 0.00723 ( 20) metal coordination : angle 3.50782 ( 24) covalent geometry : bond 0.00349 (16317) covalent geometry : angle 0.54671 (23482) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 250 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9274 (tp30) cc_final: 0.8718 (tp30) REVERT: A 108 ASN cc_start: 0.9570 (t0) cc_final: 0.9229 (t0) REVERT: C 90 ASP cc_start: 0.9097 (t0) cc_final: 0.8721 (t0) REVERT: E 59 GLU cc_start: 0.8772 (pm20) cc_final: 0.8530 (pm20) REVERT: F 53 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8626 (mm-30) REVERT: G 17 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8763 (mtm180) REVERT: H 31 LYS cc_start: 0.9180 (mptt) cc_final: 0.8906 (mmtt) REVERT: H 90 GLU cc_start: 0.9126 (mp0) cc_final: 0.8893 (mp0) REVERT: K 46 TYR cc_start: 0.8944 (t80) cc_final: 0.8592 (t80) REVERT: K 59 GLN cc_start: 0.9178 (tt0) cc_final: 0.8779 (tm-30) REVERT: K 74 THR cc_start: 0.7336 (p) cc_final: 0.7073 (t) REVERT: L 66 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7233 (pp20) REVERT: L 101 ARG cc_start: 0.8147 (ttm110) cc_final: 0.7888 (mmt90) REVERT: M 61 LEU cc_start: 0.8828 (tp) cc_final: 0.8465 (pt) outliers start: 22 outliers final: 13 residues processed: 258 average time/residue: 0.3076 time to fit residues: 111.2917 Evaluate side-chains 251 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 237 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 67 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN C 104 GLN H 81 ASN K 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.055678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035172 restraints weight = 79367.764| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.54 r_work: 0.2555 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16337 Z= 0.160 Angle : 0.568 14.269 23506 Z= 0.327 Chirality : 0.034 0.156 2728 Planarity : 0.004 0.036 1851 Dihedral : 28.522 120.223 4782 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.44 % Allowed : 21.42 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.25), residues: 1121 helix: 2.86 (0.20), residues: 652 sheet: -0.05 (0.92), residues: 36 loop : -0.68 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP L 17 HIS 0.002 0.000 HIS B 75 PHE 0.011 0.001 PHE K 38 TYR 0.023 0.001 TYR B 88 ARG 0.010 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 938) hydrogen bonds : angle 2.89658 ( 2360) metal coordination : bond 0.00789 ( 20) metal coordination : angle 3.00134 ( 24) covalent geometry : bond 0.00348 (16317) covalent geometry : angle 0.56002 (23482) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9261 (tp30) cc_final: 0.8795 (tp30) REVERT: A 108 ASN cc_start: 0.9550 (t0) cc_final: 0.9214 (t0) REVERT: B 63 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8648 (mt-10) REVERT: C 90 ASP cc_start: 0.9012 (t0) cc_final: 0.8679 (t0) REVERT: E 59 GLU cc_start: 0.8738 (pm20) cc_final: 0.8510 (pm20) REVERT: G 17 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8743 (mtm180) REVERT: H 31 LYS cc_start: 0.9151 (mptt) cc_final: 0.8851 (mmtt) REVERT: H 98 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9030 (mm) REVERT: K 46 TYR cc_start: 0.9059 (t80) cc_final: 0.8697 (t80) REVERT: K 61 HIS cc_start: 0.8414 (t70) cc_final: 0.8154 (t-90) REVERT: K 74 THR cc_start: 0.7379 (p) cc_final: 0.7148 (t) REVERT: M 61 LEU cc_start: 0.8858 (tp) cc_final: 0.8445 (pt) outliers start: 22 outliers final: 16 residues processed: 260 average time/residue: 0.3039 time to fit residues: 110.9109 Evaluate side-chains 255 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 GLN Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 106 PHE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 90 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.055130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.034628 restraints weight = 79702.891| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.52 r_work: 0.2531 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16337 Z= 0.190 Angle : 0.589 11.370 23506 Z= 0.339 Chirality : 0.035 0.175 2728 Planarity : 0.004 0.036 1851 Dihedral : 28.558 120.243 4782 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.22 % Allowed : 22.64 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.26), residues: 1121 helix: 2.78 (0.20), residues: 657 sheet: 0.01 (0.93), residues: 36 loop : -0.71 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 17 HIS 0.002 0.001 HIS B 75 PHE 0.013 0.001 PHE K 38 TYR 0.022 0.001 TYR B 88 ARG 0.008 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 938) hydrogen bonds : angle 2.95789 ( 2360) metal coordination : bond 0.00912 ( 20) metal coordination : angle 3.14787 ( 24) covalent geometry : bond 0.00422 (16317) covalent geometry : angle 0.58067 (23482) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9254 (tp30) cc_final: 0.8874 (tt0) REVERT: A 108 ASN cc_start: 0.9604 (t0) cc_final: 0.9279 (t0) REVERT: A 133 GLU cc_start: 0.8709 (mp0) cc_final: 0.8385 (mp0) REVERT: B 63 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8694 (mt-10) REVERT: C 90 ASP cc_start: 0.8975 (t0) cc_final: 0.8669 (t0) REVERT: E 59 GLU cc_start: 0.8832 (pm20) cc_final: 0.8571 (pm20) REVERT: G 17 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8783 (mtt180) REVERT: H 31 LYS cc_start: 0.9182 (mptt) cc_final: 0.8859 (mmtt) REVERT: H 98 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9055 (mm) REVERT: K 46 TYR cc_start: 0.9073 (t80) cc_final: 0.8706 (t80) REVERT: K 74 THR cc_start: 0.7361 (p) cc_final: 0.7116 (t) REVERT: K 93 ARG cc_start: 0.8723 (mtm180) cc_final: 0.8485 (mtm180) REVERT: L 66 GLU cc_start: 0.6314 (pp20) cc_final: 0.6088 (tm-30) REVERT: L 101 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7797 (mmt90) REVERT: M 61 LEU cc_start: 0.8934 (tp) cc_final: 0.8518 (pt) outliers start: 20 outliers final: 16 residues processed: 246 average time/residue: 0.3144 time to fit residues: 108.0205 Evaluate side-chains 254 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 GLN Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 1 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 0.0060 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN K 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.055861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.035874 restraints weight = 80213.481| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.48 r_work: 0.2578 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16337 Z= 0.151 Angle : 0.575 11.422 23506 Z= 0.330 Chirality : 0.034 0.168 2728 Planarity : 0.004 0.044 1851 Dihedral : 28.397 119.201 4782 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.22 % Allowed : 22.86 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.26), residues: 1121 helix: 2.80 (0.20), residues: 655 sheet: 0.14 (0.94), residues: 36 loop : -0.69 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP L 17 HIS 0.002 0.000 HIS B 75 PHE 0.014 0.001 PHE K 38 TYR 0.023 0.001 TYR B 88 ARG 0.006 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 938) hydrogen bonds : angle 2.84564 ( 2360) metal coordination : bond 0.00731 ( 20) metal coordination : angle 2.85041 ( 24) covalent geometry : bond 0.00325 (16317) covalent geometry : angle 0.56773 (23482) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9256 (tp30) cc_final: 0.8952 (tt0) REVERT: A 108 ASN cc_start: 0.9547 (t0) cc_final: 0.9210 (t0) REVERT: C 90 ASP cc_start: 0.8945 (t0) cc_final: 0.8629 (t0) REVERT: E 59 GLU cc_start: 0.8726 (pm20) cc_final: 0.8523 (pm20) REVERT: G 17 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8743 (mtm180) REVERT: H 31 LYS cc_start: 0.9138 (mptt) cc_final: 0.8817 (mmtt) REVERT: K 61 HIS cc_start: 0.8415 (t-90) cc_final: 0.8077 (t-90) REVERT: K 64 ARG cc_start: 0.8809 (mtm180) cc_final: 0.8602 (mtp180) REVERT: K 74 THR cc_start: 0.7333 (p) cc_final: 0.7095 (t) REVERT: K 93 ARG cc_start: 0.8750 (mtm180) cc_final: 0.8506 (mtm180) REVERT: L 29 GLN cc_start: 0.7476 (mm-40) cc_final: 0.6980 (mm-40) REVERT: L 97 LYS cc_start: 0.8539 (ptmm) cc_final: 0.8303 (ptmm) REVERT: L 101 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7866 (mmt90) REVERT: M 61 LEU cc_start: 0.8925 (tp) cc_final: 0.8535 (pt) REVERT: N 72 ARG cc_start: 0.7942 (ptp90) cc_final: 0.7476 (ptp90) outliers start: 20 outliers final: 17 residues processed: 252 average time/residue: 0.3131 time to fit residues: 110.2168 Evaluate side-chains 252 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 GLN Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 106 PHE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 39 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 138 optimal weight: 0.0670 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.055878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.035623 restraints weight = 80366.167| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.49 r_work: 0.2576 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16337 Z= 0.159 Angle : 0.593 11.552 23506 Z= 0.336 Chirality : 0.034 0.186 2728 Planarity : 0.004 0.036 1851 Dihedral : 28.413 119.411 4782 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.89 % Allowed : 23.31 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.25), residues: 1121 helix: 2.67 (0.20), residues: 663 sheet: 0.31 (0.96), residues: 35 loop : -0.58 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 17 HIS 0.003 0.000 HIS B 75 PHE 0.016 0.001 PHE K 38 TYR 0.022 0.001 TYR B 88 ARG 0.007 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 938) hydrogen bonds : angle 2.86400 ( 2360) metal coordination : bond 0.00756 ( 20) metal coordination : angle 3.76963 ( 24) covalent geometry : bond 0.00346 (16317) covalent geometry : angle 0.58092 (23482) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9255 (tp30) cc_final: 0.8921 (tt0) REVERT: A 108 ASN cc_start: 0.9563 (t0) cc_final: 0.9218 (t0) REVERT: A 133 GLU cc_start: 0.8697 (mp0) cc_final: 0.8362 (mp0) REVERT: C 90 ASP cc_start: 0.8908 (t0) cc_final: 0.8610 (t0) REVERT: E 59 GLU cc_start: 0.8712 (pm20) cc_final: 0.8500 (pm20) REVERT: G 17 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8769 (mtm180) REVERT: G 56 GLU cc_start: 0.8906 (tt0) cc_final: 0.8493 (tt0) REVERT: H 31 LYS cc_start: 0.9122 (mptt) cc_final: 0.8788 (mmtt) REVERT: K 46 TYR cc_start: 0.8990 (t80) cc_final: 0.8685 (t80) REVERT: K 47 LEU cc_start: 0.8517 (mm) cc_final: 0.8269 (mm) REVERT: K 61 HIS cc_start: 0.8283 (t-90) cc_final: 0.7991 (t-90) REVERT: K 74 THR cc_start: 0.7305 (p) cc_final: 0.7096 (t) REVERT: K 93 ARG cc_start: 0.8796 (mtm180) cc_final: 0.8541 (mtm180) REVERT: L 29 GLN cc_start: 0.7327 (mm-40) cc_final: 0.6959 (mm-40) REVERT: L 101 ARG cc_start: 0.8184 (ttm110) cc_final: 0.7877 (mmt90) REVERT: M 61 LEU cc_start: 0.8962 (tp) cc_final: 0.8564 (pt) outliers start: 17 outliers final: 15 residues processed: 248 average time/residue: 0.3156 time to fit residues: 109.4327 Evaluate side-chains 256 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 106 PHE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 25 ASN H 81 ASN ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.055396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034897 restraints weight = 80236.054| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.54 r_work: 0.2544 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16337 Z= 0.181 Angle : 0.603 11.828 23506 Z= 0.341 Chirality : 0.035 0.168 2728 Planarity : 0.004 0.035 1851 Dihedral : 28.501 119.729 4782 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.11 % Allowed : 23.20 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.26), residues: 1121 helix: 2.63 (0.20), residues: 664 sheet: 0.09 (0.97), residues: 34 loop : -0.55 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP L 17 HIS 0.002 0.001 HIS B 75 PHE 0.017 0.002 PHE K 38 TYR 0.025 0.001 TYR B 88 ARG 0.009 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 938) hydrogen bonds : angle 2.95489 ( 2360) metal coordination : bond 0.00730 ( 20) metal coordination : angle 3.61564 ( 24) covalent geometry : bond 0.00401 (16317) covalent geometry : angle 0.59218 (23482) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9263 (tp30) cc_final: 0.8945 (tt0) REVERT: A 108 ASN cc_start: 0.9606 (t0) cc_final: 0.9273 (t0) REVERT: C 90 ASP cc_start: 0.8894 (t0) cc_final: 0.8639 (t0) REVERT: E 59 GLU cc_start: 0.8827 (pm20) cc_final: 0.8588 (pm20) REVERT: G 17 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8783 (mtm180) REVERT: H 98 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9093 (mm) REVERT: K 46 TYR cc_start: 0.9034 (t80) cc_final: 0.8719 (t80) REVERT: K 47 LEU cc_start: 0.8617 (mm) cc_final: 0.8373 (mm) REVERT: K 61 HIS cc_start: 0.8241 (t-90) cc_final: 0.7967 (t-90) REVERT: K 93 ARG cc_start: 0.8839 (mtm180) cc_final: 0.8633 (mtm180) REVERT: L 29 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6898 (mm-40) REVERT: M 61 LEU cc_start: 0.8978 (tp) cc_final: 0.8583 (pt) REVERT: N 72 ARG cc_start: 0.8096 (ptp90) cc_final: 0.7370 (ptp90) outliers start: 19 outliers final: 14 residues processed: 247 average time/residue: 0.3206 time to fit residues: 111.0107 Evaluate side-chains 252 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 106 PHE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN ** K 76 GLN ** 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 = 0.3342 r_free = 0.3342 target = 0.054088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.033653 restraints weight = 79879.805| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.47 r_work: 0.2485 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16337 Z= 0.269 Angle : 0.668 16.323 23506 Z= 0.372 Chirality : 0.038 0.181 2728 Planarity : 0.004 0.051 1851 Dihedral : 28.773 120.752 4782 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.78 % Allowed : 23.75 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.25), residues: 1121 helix: 2.59 (0.20), residues: 657 sheet: 0.11 (0.98), residues: 34 loop : -0.57 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP M 25 HIS 0.004 0.001 HIS D 79 PHE 0.019 0.002 PHE K 38 TYR 0.027 0.002 TYR B 88 ARG 0.010 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.05492 ( 938) hydrogen bonds : angle 3.21845 ( 2360) metal coordination : bond 0.01083 ( 20) metal coordination : angle 4.35532 ( 24) covalent geometry : bond 0.00606 (16317) covalent geometry : angle 0.65385 (23482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9034.60 seconds wall clock time: 154 minutes 26.40 seconds (9266.40 seconds total)