Starting phenix.real_space_refine on Thu Sep 18 07:32:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dde_46771/09_2025/9dde_46771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dde_46771/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dde_46771/09_2025/9dde_46771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dde_46771/09_2025/9dde_46771.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dde_46771/09_2025/9dde_46771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dde_46771/09_2025/9dde_46771.map" } resolution = 3.2 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= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'HIS:plan': 1, 'ARG: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: {'ARG:plan': 2, 'GLU: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, 'ASP:plan': 1, 'ARG: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, 'PHE:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1} 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: 4.00, per 1000 atoms: 0.26 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: 1.18 Conformation dependent library (CDL) restraints added in 521.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 2.47 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: 2.61 Time building geometry restraints manager: 1.63 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.540 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- 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 : 7.35 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG D 76 TYR 0.038 0.002 TYR D 80 PHE 0.013 0.001 PHE E 78 TRP 0.005 0.001 TRP M 25 HIS 0.009 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00439 (16317) covalent geometry : angle 0.64878 (23482) hydrogen bonds : bond 0.06812 ( 938) hydrogen bonds : angle 3.32878 ( 2360) metal coordination : bond 0.01036 ( 20) metal coordination : angle 2.63993 ( 24) *********************** 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 : 0.480 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: 0.1714 time to fit residues: 71.9189 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 : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 GLN N 68 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.056046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.035475 restraints weight = 78796.657| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 3.62 r_work: 0.2537 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16337 Z= 0.211 Angle : 0.580 9.248 23506 Z= 0.341 Chirality : 0.036 0.143 2728 Planarity : 0.004 0.045 1851 Dihedral : 28.611 123.309 4782 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.89 % Allowed : 17.54 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.25), residues: 1121 helix: 2.63 (0.20), residues: 668 sheet: 0.28 (0.89), residues: 35 loop : -0.83 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 35 TYR 0.038 0.001 TYR D 80 PHE 0.019 0.002 PHE M 24 TRP 0.001 0.000 TRP L 17 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00470 (16317) covalent geometry : angle 0.57529 (23482) hydrogen bonds : bond 0.04825 ( 938) hydrogen bonds : angle 3.00149 ( 2360) metal coordination : bond 0.01623 ( 20) metal coordination : angle 2.49237 ( 24) *********************** 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 267 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9026 (m-10) cc_final: 0.8613 (m-80) REVERT: C 90 ASP cc_start: 0.9148 (t0) cc_final: 0.8848 (t0) REVERT: C 104 GLN cc_start: 0.9207 (mm-40) cc_final: 0.9006 (mm110) REVERT: E 59 GLU cc_start: 0.8780 (pm20) cc_final: 0.8567 (pm20) REVERT: F 63 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8439 (tm-30) REVERT: H 73 GLU cc_start: 0.9226 (tp30) cc_final: 0.8931 (tp30) REVERT: H 90 GLU cc_start: 0.9209 (mp0) cc_final: 0.8996 (mp0) REVERT: H 98 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9134 (mm) REVERT: K 45 ARG cc_start: 0.9725 (mmt90) cc_final: 0.9315 (mmp80) REVERT: K 74 THR cc_start: 0.7399 (p) cc_final: 0.7170 (t) REVERT: L 61 THR cc_start: 0.8753 (m) cc_final: 0.8281 (p) REVERT: L 66 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6463 (tm-30) REVERT: M 61 LEU cc_start: 0.8467 (tp) cc_final: 0.8035 (pt) outliers start: 17 outliers final: 10 residues processed: 258 average time/residue: 0.1587 time to fit residues: 56.8496 Evaluate side-chains 250 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 239 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain H residue 98 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 8 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 141 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 11 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 HIS E 125 GLN K 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.055800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.034993 restraints weight = 79807.439| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.56 r_work: 0.2531 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16337 Z= 0.194 Angle : 0.570 8.234 23506 Z= 0.335 Chirality : 0.035 0.159 2728 Planarity : 0.004 0.042 1851 Dihedral : 28.655 121.620 4782 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.33 % Allowed : 18.76 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.25), residues: 1121 helix: 2.72 (0.20), residues: 666 sheet: 0.18 (0.89), residues: 35 loop : -0.87 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 35 TYR 0.039 0.001 TYR D 80 PHE 0.025 0.002 PHE K 38 TRP 0.001 0.000 TRP M 25 HIS 0.004 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00429 (16317) covalent geometry : angle 0.56201 (23482) hydrogen bonds : bond 0.04560 ( 938) hydrogen bonds : angle 2.96371 ( 2360) metal coordination : bond 0.01251 ( 20) metal coordination : angle 3.08305 ( 24) *********************** 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 265 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9016 (tp30) cc_final: 0.8741 (tp30) REVERT: A 105 GLU cc_start: 0.9020 (tp30) cc_final: 0.8619 (tp30) REVERT: B 23 ARG cc_start: 0.9029 (ptt-90) cc_final: 0.8692 (ptp90) REVERT: B 88 TYR cc_start: 0.9011 (m-10) cc_final: 0.8728 (m-80) REVERT: C 90 ASP cc_start: 0.9128 (t0) cc_final: 0.8680 (t0) REVERT: F 24 ASP cc_start: 0.7398 (t0) cc_final: 0.7170 (t70) REVERT: G 17 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8719 (mtm180) REVERT: H 31 LYS cc_start: 0.9485 (mttt) cc_final: 0.9276 (mptt) REVERT: H 90 GLU cc_start: 0.9236 (mp0) cc_final: 0.9011 (mp0) REVERT: H 98 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9118 (mm) REVERT: K 74 THR cc_start: 0.7525 (p) cc_final: 0.7295 (t) REVERT: M 61 LEU cc_start: 0.8663 (tp) cc_final: 0.8221 (pt) outliers start: 21 outliers final: 13 residues processed: 251 average time/residue: 0.1510 time to fit residues: 52.7289 Evaluate side-chains 254 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 239 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 99 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 12 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 N residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.055068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.034534 restraints weight = 80322.342| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.56 r_work: 0.2518 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16337 Z= 0.216 Angle : 0.576 8.017 23506 Z= 0.338 Chirality : 0.036 0.155 2728 Planarity : 0.004 0.041 1851 Dihedral : 28.661 121.411 4782 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.55 % Allowed : 19.64 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.25), residues: 1121 helix: 2.67 (0.20), residues: 666 sheet: -0.21 (0.90), residues: 35 loop : -0.82 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 45 TYR 0.041 0.001 TYR D 80 PHE 0.012 0.002 PHE E 78 TRP 0.002 0.000 TRP M 25 HIS 0.004 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00481 (16317) covalent geometry : angle 0.56844 (23482) hydrogen bonds : bond 0.04885 ( 938) hydrogen bonds : angle 3.04941 ( 2360) metal coordination : bond 0.01266 ( 20) metal coordination : angle 3.01729 ( 24) *********************** 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 263 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9038 (tp30) cc_final: 0.8551 (tp30) REVERT: B 63 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8678 (mt-10) REVERT: B 84 MET cc_start: 0.8835 (tpp) cc_final: 0.8628 (tpp) REVERT: B 88 TYR cc_start: 0.9021 (m-10) cc_final: 0.8666 (m-80) REVERT: E 59 GLU cc_start: 0.8918 (pm20) cc_final: 0.8700 (pm20) REVERT: G 17 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8764 (mtt180) REVERT: H 31 LYS cc_start: 0.9468 (mttt) cc_final: 0.9266 (mptt) REVERT: K 27 ASP cc_start: 0.7866 (p0) cc_final: 0.7451 (p0) REVERT: K 74 THR cc_start: 0.7437 (p) cc_final: 0.7200 (t) REVERT: M 61 LEU cc_start: 0.8866 (tp) cc_final: 0.8460 (pt) outliers start: 23 outliers final: 17 residues processed: 245 average time/residue: 0.1518 time to fit residues: 51.7720 Evaluate side-chains 249 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 95 VAL 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 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 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 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 103 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 0.0010 chunk 70 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS K 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.055711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.035197 restraints weight = 79409.055| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.56 r_work: 0.2553 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16337 Z= 0.166 Angle : 0.559 8.932 23506 Z= 0.327 Chirality : 0.034 0.152 2728 Planarity : 0.004 0.039 1851 Dihedral : 28.449 120.704 4782 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.77 % Allowed : 20.09 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.26), residues: 1121 helix: 2.77 (0.20), residues: 664 sheet: -0.04 (0.92), residues: 36 loop : -0.69 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 67 TYR 0.025 0.001 TYR D 80 PHE 0.010 0.001 PHE K 38 TRP 0.001 0.000 TRP L 17 HIS 0.003 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00362 (16317) covalent geometry : angle 0.54949 (23482) hydrogen bonds : bond 0.04177 ( 938) hydrogen bonds : angle 2.86169 ( 2360) metal coordination : bond 0.01015 ( 20) metal coordination : angle 3.26751 ( 24) *********************** 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 269 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9056 (tp30) cc_final: 0.8545 (tp30) REVERT: C 90 ASP cc_start: 0.9054 (t0) cc_final: 0.8801 (t0) REVERT: E 59 GLU cc_start: 0.8782 (pm20) cc_final: 0.8542 (pm20) REVERT: G 17 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8723 (mtm180) REVERT: H 98 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9069 (mm) REVERT: K 59 GLN cc_start: 0.9218 (tt0) cc_final: 0.8840 (tm-30) REVERT: K 74 THR cc_start: 0.7404 (p) cc_final: 0.7171 (t) REVERT: M 61 LEU cc_start: 0.8906 (tp) cc_final: 0.8495 (pt) outliers start: 25 outliers final: 19 residues processed: 252 average time/residue: 0.1503 time to fit residues: 52.9884 Evaluate side-chains 253 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE 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 43 VAL 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 31 ILE Chi-restraints excluded: chain K residue 66 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 Chi-restraints excluded: chain O residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 68 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 94 ASN F 25 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 = 0.3353 r_free = 0.3353 target = 0.054456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.033910 restraints weight = 80513.580| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 3.57 r_work: 0.2496 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16337 Z= 0.247 Angle : 0.605 9.524 23506 Z= 0.350 Chirality : 0.037 0.159 2728 Planarity : 0.004 0.040 1851 Dihedral : 28.751 122.397 4782 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.44 % Allowed : 20.09 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.25), residues: 1121 helix: 2.75 (0.20), residues: 658 sheet: -0.17 (0.99), residues: 34 loop : -0.65 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 101 TYR 0.045 0.002 TYR D 80 PHE 0.013 0.002 PHE K 38 TRP 0.002 0.000 TRP M 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00554 (16317) covalent geometry : angle 0.59459 (23482) hydrogen bonds : bond 0.05249 ( 938) hydrogen bonds : angle 3.13252 ( 2360) metal coordination : bond 0.01736 ( 20) metal coordination : angle 3.47572 ( 24) *********************** 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 266 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9047 (tp30) cc_final: 0.8555 (tp30) REVERT: C 90 ASP cc_start: 0.9084 (t0) cc_final: 0.8818 (t0) REVERT: E 59 GLU cc_start: 0.8877 (pm20) cc_final: 0.8676 (pm20) REVERT: F 63 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8723 (tm-30) REVERT: F 67 ARG cc_start: 0.9259 (ttp80) cc_final: 0.8911 (ttm110) REVERT: G 17 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8792 (mtt180) REVERT: H 31 LYS cc_start: 0.9239 (mptt) cc_final: 0.8969 (mmtt) REVERT: H 87 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8821 (p) REVERT: M 61 LEU cc_start: 0.8969 (tp) cc_final: 0.8532 (pt) outliers start: 31 outliers final: 21 residues processed: 247 average time/residue: 0.1510 time to fit residues: 52.1671 Evaluate side-chains 250 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 95 VAL 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 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 66 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 5 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 76 GLN ** 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 = 0.3391 r_free = 0.3391 target = 0.055626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.035604 restraints weight = 79754.575| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.50 r_work: 0.2562 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16337 Z= 0.159 Angle : 0.579 14.174 23506 Z= 0.332 Chirality : 0.034 0.156 2728 Planarity : 0.004 0.038 1851 Dihedral : 28.484 119.548 4782 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.44 % Allowed : 22.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.26), residues: 1121 helix: 2.74 (0.20), residues: 663 sheet: 0.22 (1.00), residues: 34 loop : -0.58 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 101 TYR 0.022 0.001 TYR D 80 PHE 0.013 0.001 PHE K 38 TRP 0.001 0.000 TRP L 17 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00345 (16317) covalent geometry : angle 0.57149 (23482) hydrogen bonds : bond 0.04026 ( 938) hydrogen bonds : angle 2.87242 ( 2360) metal coordination : bond 0.01166 ( 20) metal coordination : angle 2.97080 ( 24) *********************** 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 262 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9049 (tp30) cc_final: 0.8512 (tp30) REVERT: A 108 ASN cc_start: 0.9565 (t0) cc_final: 0.9258 (t0) REVERT: A 133 GLU cc_start: 0.8767 (mp0) cc_final: 0.8404 (mp0) REVERT: B 63 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8626 (mt-10) REVERT: C 90 ASP cc_start: 0.9000 (t0) cc_final: 0.8749 (t0) REVERT: G 17 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8659 (mtt180) REVERT: H 73 GLU cc_start: 0.9268 (tp30) cc_final: 0.9054 (tp30) REVERT: M 61 LEU cc_start: 0.8980 (tp) cc_final: 0.8579 (pt) outliers start: 22 outliers final: 18 residues processed: 248 average time/residue: 0.1503 time to fit residues: 51.8983 Evaluate side-chains 251 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 98 LEU 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 K residue 12 LEU Chi-restraints excluded: chain K residue 66 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 O residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 125 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 104 GLN H 81 ASN K 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.055653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.035343 restraints weight = 80592.773| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.52 r_work: 0.2560 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16337 Z= 0.163 Angle : 0.586 11.779 23506 Z= 0.335 Chirality : 0.034 0.157 2728 Planarity : 0.004 0.050 1851 Dihedral : 28.505 119.985 4782 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.89 % Allowed : 23.75 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.26), residues: 1121 helix: 2.73 (0.20), residues: 661 sheet: 0.29 (1.06), residues: 32 loop : -0.53 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 72 TYR 0.026 0.001 TYR D 80 PHE 0.014 0.001 PHE K 38 TRP 0.001 0.000 TRP L 17 HIS 0.005 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00356 (16317) covalent geometry : angle 0.57870 (23482) hydrogen bonds : bond 0.04084 ( 938) hydrogen bonds : angle 2.88360 ( 2360) metal coordination : bond 0.00743 ( 20) metal coordination : angle 2.93943 ( 24) *********************** 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 261 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9046 (tp30) cc_final: 0.8506 (tp30) REVERT: A 108 ASN cc_start: 0.9564 (t0) cc_final: 0.9247 (t0) REVERT: C 90 ASP cc_start: 0.8974 (t0) cc_final: 0.8715 (t0) REVERT: G 56 GLU cc_start: 0.8931 (tt0) cc_final: 0.8534 (tt0) REVERT: K 61 HIS cc_start: 0.8673 (t70) cc_final: 0.8398 (t-90) REVERT: M 56 ARG cc_start: 0.8883 (tpt170) cc_final: 0.8507 (mmp80) REVERT: M 61 LEU cc_start: 0.9047 (tp) cc_final: 0.8648 (pt) outliers start: 17 outliers final: 14 residues processed: 251 average time/residue: 0.1422 time to fit residues: 50.5310 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 99 LEU 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 M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 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 130 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.055998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035808 restraints weight = 80566.594| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.54 r_work: 0.2580 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16337 Z= 0.155 Angle : 0.592 11.368 23506 Z= 0.338 Chirality : 0.034 0.156 2728 Planarity : 0.004 0.038 1851 Dihedral : 28.409 119.327 4782 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.78 % Allowed : 25.19 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.25), residues: 1121 helix: 2.71 (0.20), residues: 661 sheet: -1.73 (1.13), residues: 22 loop : -0.54 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 72 TYR 0.024 0.001 TYR D 80 PHE 0.015 0.001 PHE K 38 TRP 0.000 0.000 TRP L 17 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00337 (16317) covalent geometry : angle 0.58560 (23482) hydrogen bonds : bond 0.03872 ( 938) hydrogen bonds : angle 2.85249 ( 2360) metal coordination : bond 0.00620 ( 20) metal coordination : angle 2.86720 ( 24) *********************** 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 260 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9542 (t0) cc_final: 0.9195 (t0) REVERT: A 133 GLU cc_start: 0.8775 (mp0) cc_final: 0.8425 (mp0) REVERT: C 90 ASP cc_start: 0.8944 (t0) cc_final: 0.8718 (t0) REVERT: D 81 ASN cc_start: 0.8896 (m-40) cc_final: 0.8676 (m-40) REVERT: G 56 GLU cc_start: 0.8913 (tt0) cc_final: 0.8524 (tt0) REVERT: K 61 HIS cc_start: 0.8606 (t70) cc_final: 0.8306 (t-90) REVERT: K 93 ARG cc_start: 0.8814 (mtm180) cc_final: 0.8571 (mtm180) REVERT: L 29 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7019 (mm-40) REVERT: M 61 LEU cc_start: 0.9065 (tp) cc_final: 0.8637 (pt) outliers start: 16 outliers final: 15 residues processed: 250 average time/residue: 0.1556 time to fit residues: 54.4141 Evaluate side-chains 252 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 114 VAL 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 Chi-restraints excluded: chain O residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 104 optimal weight: 50.0000 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 81 ASN ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.053798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.033294 restraints weight = 80764.594| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 3.54 r_work: 0.2466 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 16337 Z= 0.306 Angle : 0.697 16.652 23506 Z= 0.390 Chirality : 0.040 0.180 2728 Planarity : 0.005 0.058 1851 Dihedral : 28.949 121.365 4782 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.78 % Allowed : 24.86 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.25), residues: 1121 helix: 2.56 (0.20), residues: 659 sheet: 0.33 (1.05), residues: 32 loop : -0.64 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 56 TYR 0.056 0.002 TYR D 80 PHE 0.018 0.002 PHE K 38 TRP 0.004 0.001 TRP M 25 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00692 (16317) covalent geometry : angle 0.68114 (23482) hydrogen bonds : bond 0.05893 ( 938) hydrogen bonds : angle 3.34717 ( 2360) metal coordination : bond 0.01388 ( 20) metal coordination : angle 4.74242 ( 24) ********************** 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 241 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 225 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9070 (tp30) cc_final: 0.8647 (tp30) REVERT: C 90 ASP cc_start: 0.8931 (t0) cc_final: 0.8705 (t0) REVERT: F 53 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8832 (mm-30) REVERT: K 70 ARG cc_start: 0.7337 (mmp80) cc_final: 0.7066 (mmp80) REVERT: K 93 ARG cc_start: 0.8790 (mtm180) cc_final: 0.8551 (mtm180) REVERT: L 29 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6927 (mm-40) REVERT: L 97 LYS cc_start: 0.8677 (ptmm) cc_final: 0.8439 (pttm) REVERT: M 61 LEU cc_start: 0.9047 (tp) cc_final: 0.8629 (pt) outliers start: 16 outliers final: 14 residues processed: 231 average time/residue: 0.1593 time to fit residues: 51.0259 Evaluate side-chains 234 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 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 5 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 74 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 76 GLN ** 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 = 0.3378 r_free = 0.3378 target = 0.054979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.034983 restraints weight = 80789.464| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.41 r_work: 0.2554 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16337 Z= 0.180 Angle : 0.625 16.538 23506 Z= 0.353 Chirality : 0.035 0.169 2728 Planarity : 0.004 0.037 1851 Dihedral : 28.554 119.466 4782 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.66 % Allowed : 25.31 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.26), residues: 1121 helix: 2.73 (0.20), residues: 659 sheet: 0.28 (1.02), residues: 32 loop : -0.56 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 70 TYR 0.034 0.001 TYR D 80 PHE 0.020 0.001 PHE K 38 TRP 0.001 0.000 TRP L 17 HIS 0.004 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00397 (16317) covalent geometry : angle 0.61377 (23482) hydrogen bonds : bond 0.04332 ( 938) hydrogen bonds : angle 2.94479 ( 2360) metal coordination : bond 0.00829 ( 20) metal coordination : angle 3.73280 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4635.87 seconds wall clock time: 79 minutes 42.70 seconds (4782.70 seconds total)