Starting phenix.real_space_refine on Thu Feb 13 07:15:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8z_36082/02_2025/8j8z_36082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8z_36082/02_2025/8j8z_36082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8z_36082/02_2025/8j8z_36082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8z_36082/02_2025/8j8z_36082.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8z_36082/02_2025/8j8z_36082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8z_36082/02_2025/8j8z_36082.cif" } resolution = 3.4 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= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 34 5.16 5 C 5564 2.51 5 N 1458 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8722 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2601 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 25, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "H" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 898 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2607 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "I" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 895 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 795 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 3} Unresolved non-hydrogen planarities: 12 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 5.65, per 1000 atoms: 0.65 Number of scatterers: 8722 At special positions: 0 Unit cell: (81.9448, 144.867, 90.7246, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 6 15.00 O 1660 8.00 N 1458 7.00 C 5564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.04 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 24 sheets defined 6.4% alpha, 47.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'I' and resid 31 through 33 No H-bonds generated for 'chain 'I' and resid 31 through 33' Processing helix chain 'I' and resid 65 through 68 Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.739A pdb=" N THR I 94 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 removed outlier: 3.880A pdb=" N PHE M 84 " --> pdb=" O PRO M 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117 removed outlier: 3.760A pdb=" N PHE A 115 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 39 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 22 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 10 " --> pdb=" O GLU V 349 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 29 removed outlier: 5.758A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 85 removed outlier: 5.807A pdb=" N ARG A 76 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR A 63 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 80 " --> pdb=" O CYS A 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 85 removed outlier: 5.807A pdb=" N ARG A 76 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR A 63 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 80 " --> pdb=" O CYS A 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 190 removed outlier: 4.651A pdb=" N PHE A 190 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS A 195 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 270 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.228A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.228A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 7 through 10 removed outlier: 3.639A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 13 through 14 Processing sheet with id=AB1, first strand: chain 'H' and resid 61 through 63 removed outlier: 5.333A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.660A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.660A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 112 through 117 removed outlier: 3.791A pdb=" N PHE B 115 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 39 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 10 " --> pdb=" O GLU U 349 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 26 through 29 removed outlier: 5.943A pdb=" N PHE B 27 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE B 61 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 78 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 26 through 29 removed outlier: 5.943A pdb=" N PHE B 27 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 183 through 188 Processing sheet with id=AB9, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.248A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE B 231 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU B 257 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE B 233 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N MET B 255 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 235 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 7 through 10 Processing sheet with id=AC2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.841A pdb=" N GLY I 13 " --> pdb=" O THR I 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 60 through 63 removed outlier: 3.623A pdb=" N TYR I 60 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TRP I 50 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG I 41 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA I 52 " --> pdb=" O TRP I 39 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR I 112 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ARG I 103 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N LEU I 110 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AC5, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.934A pdb=" N LEU M 12 " --> pdb=" O GLU M 106 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR M 87 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.934A pdb=" N LEU M 12 " --> pdb=" O GLU M 106 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR M 87 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR M 98 " --> pdb=" O GLN M 91 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 2.69 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: 2099 1.33 - 1.45: 1728 1.45 - 1.57: 5030 1.57 - 1.69: 16 1.69 - 1.81: 44 Bond restraints: 8917 Sorted by residual: bond pdb=" O1P SEP V 348 " pdb=" P SEP V 348 " ideal model delta sigma weight residual 1.610 1.504 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O3P SEP U 351 " pdb=" P SEP U 351 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" O3P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" O1P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O2P SEP U 351 " pdb=" P SEP U 351 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.51e+01 ... (remaining 8912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 11729 1.74 - 3.48: 331 3.48 - 5.22: 73 5.22 - 6.95: 6 6.95 - 8.69: 7 Bond angle restraints: 12146 Sorted by residual: angle pdb=" CA PRO A 180 " pdb=" N PRO A 180 " pdb=" CD PRO A 180 " ideal model delta sigma weight residual 112.00 104.52 7.48 1.40e+00 5.10e-01 2.85e+01 angle pdb=" C GLN M 39 " pdb=" CA GLN M 39 " pdb=" CB GLN M 39 " ideal model delta sigma weight residual 111.77 103.75 8.02 1.52e+00 4.33e-01 2.78e+01 angle pdb=" C SER L 31 " pdb=" CA SER L 31 " pdb=" CB SER L 31 " ideal model delta sigma weight residual 116.34 110.85 5.49 1.40e+00 5.10e-01 1.54e+01 angle pdb=" CA GLN M 90 " pdb=" C GLN M 90 " pdb=" O GLN M 90 " ideal model delta sigma weight residual 120.32 116.33 3.99 1.11e+00 8.12e-01 1.30e+01 angle pdb=" CA TYR M 37 " pdb=" C TYR M 37 " pdb=" O TYR M 37 " ideal model delta sigma weight residual 120.66 116.72 3.94 1.15e+00 7.56e-01 1.18e+01 ... (remaining 12141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4905 17.85 - 35.70: 336 35.70 - 53.56: 87 53.56 - 71.41: 19 71.41 - 89.26: 11 Dihedral angle restraints: 5358 sinusoidal: 2023 harmonic: 3335 Sorted by residual: dihedral pdb=" CB CYS I 25 " pdb=" SG CYS I 25 " pdb=" SG CYS I 99 " pdb=" CB CYS I 99 " ideal model delta sinusoidal sigma weight residual 93.00 58.38 34.62 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" C TYR M 37 " pdb=" N TYR M 37 " pdb=" CA TYR M 37 " pdb=" CB TYR M 37 " ideal model delta harmonic sigma weight residual -122.60 -114.13 -8.47 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" CA LYS I 79 " pdb=" C LYS I 79 " pdb=" N ASN I 80 " pdb=" CA ASN I 80 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1227 0.066 - 0.132: 163 0.132 - 0.198: 4 0.198 - 0.264: 3 0.264 - 0.331: 2 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CA ILE U 352 " pdb=" N ILE U 352 " pdb=" C ILE U 352 " pdb=" CB ILE U 352 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA TYR B 249 " pdb=" N TYR B 249 " pdb=" C TYR B 249 " pdb=" CB TYR B 249 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA TYR M 37 " pdb=" N TYR M 37 " pdb=" C TYR M 37 " pdb=" CB TYR M 37 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1396 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS V 347 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C CYS V 347 " 0.036 2.00e-02 2.50e+03 pdb=" O CYS V 347 " -0.014 2.00e-02 2.50e+03 pdb=" N SEP V 348 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 251 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO B 252 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 252 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 252 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 179 " -0.031 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 180 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.025 5.00e-02 4.00e+02 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 239 2.67 - 3.23: 8409 3.23 - 3.79: 12361 3.79 - 4.34: 17170 4.34 - 4.90: 29731 Nonbonded interactions: 67910 Sorted by model distance: nonbonded pdb=" N GLU B 50 " pdb=" OE1 GLU B 50 " model vdw 2.118 3.120 nonbonded pdb=" N GLU L 82 " pdb=" OE1 GLU L 82 " model vdw 2.239 3.120 nonbonded pdb=" N GLU M 82 " pdb=" OE1 GLU M 82 " model vdw 2.274 3.120 nonbonded pdb=" O LEU A 68 " pdb=" ND2 ASN B 245 " model vdw 2.299 3.120 nonbonded pdb=" O ASN H 87 " pdb=" OG SER H 88 " model vdw 2.302 3.040 ... (remaining 67905 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 6 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 66 or (resid 67 and (name N or name \ CA or name C or name O or name CB )) or resid 68 or (resid 69 and (name N or na \ me CA or name C or name O or name CB )) or resid 70 through 133 or (resid 134 th \ rough 135 and (name N or name CA or name C or name O or name CB )) or resid 136 \ through 159 or (resid 160 through 161 and (name N or name CA or name C or name O \ or name CB )) or resid 162 through 175 or (resid 176 through 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 357)) selection = (chain 'B' and (resid 6 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 76 or (resid 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 134 or (resid 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 through 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 through 176 or (resid 177 and (name N or name CA or name C or name O or name C \ B )) or resid 178 through 214 or (resid 215 and (name N or name CA or name C or \ name O or name CB )) or resid 216 through 248 or (resid 249 and (name N or name \ CA or name C or name O or name CB )) or resid 250 through 284 or (resid 285 and \ (name N or name CA or name C or name O or name CB )) or resid 286 through 357)) } ncs_group { reference = (chain 'H' and (resid 5 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 121)) selection = chain 'I' } ncs_group { reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 50 or (resid 51 through 52 and (name N \ or name CA or name C or name O or name CB )) or resid 53 through 89 or (resid 9 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 91 through 1 \ 07)) selection = chain 'M' } ncs_group { reference = chain 'U' selection = chain 'V' } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.590 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.006 0.118 8917 Z= 0.341 Angle : 0.730 8.694 12146 Z= 0.399 Chirality : 0.047 0.331 1399 Planarity : 0.004 0.046 1538 Dihedral : 14.135 89.261 3202 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.86 % Allowed : 13.89 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.49 (0.26), residues: 1112 helix: -1.05 (0.79), residues: 36 sheet: -0.30 (0.23), residues: 526 loop : -0.13 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 50 HIS 0.006 0.001 HIS A 159 PHE 0.012 0.001 PHE M 99 TYR 0.016 0.001 TYR L 94 ARG 0.005 0.001 ARG M 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 1.070 Fit side-chains REVERT: H 33 TYR cc_start: 0.8669 (m-80) cc_final: 0.8368 (m-80) REVERT: H 49 GLU cc_start: 0.8121 (tt0) cc_final: 0.7808 (pt0) REVERT: L 106 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7067 (mt-10) REVERT: B 272 TYR cc_start: 0.7460 (m-80) cc_final: 0.7086 (m-10) REVERT: B 321 TYR cc_start: 0.8221 (m-80) cc_final: 0.7774 (m-80) REVERT: I 33 TYR cc_start: 0.8730 (m-80) cc_final: 0.8390 (m-80) REVERT: I 79 LYS cc_start: 0.8276 (ptpp) cc_final: 0.8071 (ptpp) REVERT: I 102 SER cc_start: 0.9151 (t) cc_final: 0.8880 (p) REVERT: M 28 GLN cc_start: 0.7027 (mp10) cc_final: 0.6653 (mp10) outliers start: 8 outliers final: 5 residues processed: 148 average time/residue: 0.2220 time to fit residues: 45.3080 Evaluate side-chains 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain U residue 347 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN L 28 GLN L 39 GLN B 219 HIS I 42 GLN M 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.139939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112598 restraints weight = 14480.480| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.97 r_work: 0.3335 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8917 Z= 0.308 Angle : 0.672 6.433 12146 Z= 0.346 Chirality : 0.047 0.149 1399 Planarity : 0.004 0.037 1538 Dihedral : 6.338 54.885 1261 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.72 % Allowed : 14.75 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.33 (0.26), residues: 1112 helix: -0.52 (0.86), residues: 36 sheet: -0.18 (0.22), residues: 554 loop : -0.05 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 50 HIS 0.005 0.001 HIS A 159 PHE 0.016 0.002 PHE A 268 TYR 0.014 0.002 TYR A 238 ARG 0.007 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.988 Fit side-chains REVERT: A 144 TYR cc_start: 0.7843 (m-80) cc_final: 0.7195 (m-10) REVERT: A 255 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8190 (tmm) REVERT: A 321 TYR cc_start: 0.8499 (m-80) cc_final: 0.8194 (m-80) REVERT: H 33 TYR cc_start: 0.8765 (m-80) cc_final: 0.8416 (m-80) REVERT: H 49 GLU cc_start: 0.8244 (tt0) cc_final: 0.7792 (pt0) REVERT: L 5 MET cc_start: 0.9074 (mmt) cc_final: 0.8265 (mmt) REVERT: L 83 ASP cc_start: 0.6863 (m-30) cc_final: 0.6570 (m-30) REVERT: L 106 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7049 (mt-10) REVERT: B 255 MET cc_start: 0.8221 (tmm) cc_final: 0.7974 (tmm) REVERT: B 321 TYR cc_start: 0.8509 (m-80) cc_final: 0.8188 (m-80) REVERT: I 33 TYR cc_start: 0.8720 (m-80) cc_final: 0.8338 (m-80) REVERT: I 87 ASN cc_start: 0.7970 (m-40) cc_final: 0.7744 (m-40) REVERT: M 28 GLN cc_start: 0.7375 (mp10) cc_final: 0.6997 (mp10) REVERT: M 56 TYR cc_start: 0.8483 (t80) cc_final: 0.8189 (t80) outliers start: 16 outliers final: 10 residues processed: 151 average time/residue: 0.2007 time to fit residues: 42.4170 Evaluate side-chains 127 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN L 28 GLN L 38 GLN M 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113457 restraints weight = 14661.244| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.99 r_work: 0.3353 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8917 Z= 0.252 Angle : 0.617 5.331 12146 Z= 0.318 Chirality : 0.046 0.154 1399 Planarity : 0.004 0.036 1538 Dihedral : 6.071 57.803 1252 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.23 % Allowed : 14.85 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.34 (0.26), residues: 1112 helix: -0.29 (0.89), residues: 36 sheet: -0.23 (0.22), residues: 572 loop : -0.01 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 50 HIS 0.004 0.001 HIS B 353 PHE 0.014 0.002 PHE A 268 TYR 0.015 0.001 TYR B 272 ARG 0.008 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.067 Fit side-chains REVERT: A 62 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6780 (ptp90) REVERT: A 321 TYR cc_start: 0.8590 (m-80) cc_final: 0.8196 (m-80) REVERT: H 22 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7715 (ttt90) REVERT: H 33 TYR cc_start: 0.8519 (m-80) cc_final: 0.8290 (m-80) REVERT: H 41 ARG cc_start: 0.8659 (ptt180) cc_final: 0.7990 (ptm160) REVERT: H 87 ASN cc_start: 0.7801 (m-40) cc_final: 0.7552 (m-40) REVERT: B 75 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7637 (p90) REVERT: B 255 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7893 (tmm) REVERT: B 314 ILE cc_start: 0.7755 (mm) cc_final: 0.7325 (mp) REVERT: B 321 TYR cc_start: 0.8449 (m-80) cc_final: 0.8142 (m-80) REVERT: I 33 TYR cc_start: 0.8684 (m-80) cc_final: 0.8306 (m-80) REVERT: I 41 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8030 (ptt180) REVERT: I 89 LEU cc_start: 0.8035 (mm) cc_final: 0.7703 (mm) REVERT: I 93 ASP cc_start: 0.7443 (p0) cc_final: 0.7240 (p0) REVERT: M 28 GLN cc_start: 0.7131 (mp10) cc_final: 0.6767 (mp10) outliers start: 30 outliers final: 17 residues processed: 159 average time/residue: 0.2107 time to fit residues: 46.4628 Evaluate side-chains 145 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.0670 chunk 67 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN L 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.145024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118659 restraints weight = 13777.713| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.72 r_work: 0.3421 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8917 Z= 0.182 Angle : 0.563 5.297 12146 Z= 0.290 Chirality : 0.044 0.139 1399 Planarity : 0.004 0.038 1538 Dihedral : 5.875 60.332 1252 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.58 % Allowed : 17.01 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.23 (0.26), residues: 1112 helix: -0.19 (0.90), residues: 36 sheet: -0.09 (0.22), residues: 568 loop : -0.02 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 50 HIS 0.003 0.001 HIS B 353 PHE 0.015 0.001 PHE B 87 TYR 0.010 0.001 TYR A 54 ARG 0.005 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.956 Fit side-chains REVERT: A 321 TYR cc_start: 0.8602 (m-80) cc_final: 0.8243 (m-80) REVERT: H 22 ARG cc_start: 0.7846 (ttt90) cc_final: 0.7560 (ttt90) REVERT: H 33 TYR cc_start: 0.8518 (m-80) cc_final: 0.8276 (m-80) REVERT: H 41 ARG cc_start: 0.8504 (ptt180) cc_final: 0.7896 (ptm160) REVERT: H 87 ASN cc_start: 0.7785 (m-40) cc_final: 0.7532 (m-40) REVERT: B 75 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7449 (p90) REVERT: B 255 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7983 (tmm) REVERT: B 314 ILE cc_start: 0.7804 (mm) cc_final: 0.7438 (mp) REVERT: B 321 TYR cc_start: 0.8496 (m-80) cc_final: 0.8099 (m-80) REVERT: I 33 TYR cc_start: 0.8627 (m-80) cc_final: 0.8359 (m-80) REVERT: I 41 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7999 (ptt180) REVERT: I 89 LEU cc_start: 0.7933 (mm) cc_final: 0.7626 (mm) REVERT: I 93 ASP cc_start: 0.7416 (p0) cc_final: 0.7208 (p0) REVERT: M 28 GLN cc_start: 0.7088 (mp10) cc_final: 0.6716 (mp10) outliers start: 24 outliers final: 12 residues processed: 160 average time/residue: 0.2034 time to fit residues: 45.3048 Evaluate side-chains 141 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 2 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 0.0570 chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 82 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.144518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118709 restraints weight = 13742.847| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.65 r_work: 0.3422 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8917 Z= 0.204 Angle : 0.577 8.847 12146 Z= 0.295 Chirality : 0.044 0.139 1399 Planarity : 0.004 0.038 1538 Dihedral : 5.836 60.987 1252 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.77 % Allowed : 17.33 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.24 (0.26), residues: 1112 helix: -0.17 (0.89), residues: 36 sheet: -0.14 (0.22), residues: 574 loop : 0.03 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 50 HIS 0.003 0.001 HIS B 353 PHE 0.011 0.001 PHE A 268 TYR 0.013 0.001 TYR B 272 ARG 0.005 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.971 Fit side-chains REVERT: A 321 TYR cc_start: 0.8582 (m-80) cc_final: 0.8207 (m-80) REVERT: H 33 TYR cc_start: 0.8668 (m-80) cc_final: 0.8464 (m-80) REVERT: H 41 ARG cc_start: 0.8533 (ptt180) cc_final: 0.7806 (ptm160) REVERT: H 87 ASN cc_start: 0.7795 (m-40) cc_final: 0.7525 (m-40) REVERT: H 93 ASP cc_start: 0.5999 (m-30) cc_final: 0.5616 (m-30) REVERT: B 75 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7494 (p90) REVERT: B 255 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8000 (tmm) REVERT: B 314 ILE cc_start: 0.7837 (mm) cc_final: 0.7449 (mp) REVERT: B 321 TYR cc_start: 0.8419 (m-80) cc_final: 0.7967 (m-80) REVERT: I 41 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8011 (ptt180) REVERT: M 28 GLN cc_start: 0.7188 (mp10) cc_final: 0.6878 (mp10) outliers start: 35 outliers final: 16 residues processed: 154 average time/residue: 0.2101 time to fit residues: 44.4445 Evaluate side-chains 142 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain V residue 353 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN B 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.140948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113739 restraints weight = 14437.192| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.97 r_work: 0.3356 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8917 Z= 0.276 Angle : 0.613 7.733 12146 Z= 0.312 Chirality : 0.045 0.147 1399 Planarity : 0.004 0.038 1538 Dihedral : 5.945 60.766 1252 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.77 % Allowed : 17.65 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.18 (0.26), residues: 1112 helix: 2.01 (1.01), residues: 24 sheet: -0.19 (0.22), residues: 574 loop : 0.06 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 50 HIS 0.004 0.001 HIS B 353 PHE 0.016 0.002 PHE B 277 TYR 0.012 0.001 TYR A 238 ARG 0.010 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.994 Fit side-chains REVERT: A 166 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6092 (mt) REVERT: A 321 TYR cc_start: 0.8585 (m-80) cc_final: 0.8237 (m-80) REVERT: H 22 ARG cc_start: 0.7791 (ttt90) cc_final: 0.7507 (ttt90) REVERT: H 33 TYR cc_start: 0.8545 (m-80) cc_final: 0.8273 (m-80) REVERT: H 87 ASN cc_start: 0.7843 (m-40) cc_final: 0.7587 (m-40) REVERT: H 93 ASP cc_start: 0.6196 (m-30) cc_final: 0.5788 (m-30) REVERT: B 75 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7724 (p90) REVERT: B 177 ARG cc_start: 0.7862 (tmm160) cc_final: 0.7639 (tmm160) REVERT: B 314 ILE cc_start: 0.7935 (mm) cc_final: 0.7594 (mp) REVERT: B 321 TYR cc_start: 0.8443 (m-80) cc_final: 0.8060 (m-80) REVERT: I 33 TYR cc_start: 0.8352 (m-80) cc_final: 0.7957 (m-80) REVERT: I 41 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8043 (ptt180) REVERT: M 28 GLN cc_start: 0.7235 (mp10) cc_final: 0.6831 (mp10) outliers start: 35 outliers final: 26 residues processed: 150 average time/residue: 0.1988 time to fit residues: 42.4965 Evaluate side-chains 153 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain M residue 2 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 96 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.141665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114582 restraints weight = 14499.041| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.96 r_work: 0.3367 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8917 Z= 0.232 Angle : 0.586 7.108 12146 Z= 0.298 Chirality : 0.044 0.144 1399 Planarity : 0.004 0.039 1538 Dihedral : 5.871 62.145 1252 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.55 % Allowed : 17.87 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.14 (0.26), residues: 1112 helix: 2.15 (1.03), residues: 24 sheet: -0.18 (0.22), residues: 574 loop : 0.10 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 50 HIS 0.004 0.001 HIS B 353 PHE 0.013 0.001 PHE B 277 TYR 0.012 0.001 TYR B 272 ARG 0.008 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.127 Fit side-chains REVERT: A 166 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.6094 (mt) REVERT: A 321 TYR cc_start: 0.8604 (m-80) cc_final: 0.8316 (m-80) REVERT: H 22 ARG cc_start: 0.7748 (ttt90) cc_final: 0.7530 (ttt90) REVERT: H 33 TYR cc_start: 0.8530 (m-80) cc_final: 0.8183 (m-80) REVERT: H 41 ARG cc_start: 0.8809 (ptt-90) cc_final: 0.8005 (ptm160) REVERT: H 87 ASN cc_start: 0.7834 (m-40) cc_final: 0.7581 (m-40) REVERT: H 93 ASP cc_start: 0.6089 (m-30) cc_final: 0.5760 (m-30) REVERT: B 75 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7713 (p90) REVERT: B 177 ARG cc_start: 0.7809 (tmm160) cc_final: 0.7569 (tmm160) REVERT: B 242 CYS cc_start: 0.8227 (OUTLIER) cc_final: 0.8007 (p) REVERT: B 314 ILE cc_start: 0.7824 (mm) cc_final: 0.7414 (mp) REVERT: B 321 TYR cc_start: 0.8471 (m-80) cc_final: 0.8052 (m-80) REVERT: I 33 TYR cc_start: 0.8613 (m-80) cc_final: 0.8215 (m-80) REVERT: I 41 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7994 (ptt180) REVERT: M 28 GLN cc_start: 0.7279 (mp10) cc_final: 0.6891 (mp10) outliers start: 33 outliers final: 25 residues processed: 149 average time/residue: 0.2067 time to fit residues: 43.6618 Evaluate side-chains 152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 108 optimal weight: 0.1980 chunk 24 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115619 restraints weight = 14606.535| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.97 r_work: 0.3402 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8917 Z= 0.192 Angle : 0.573 6.683 12146 Z= 0.291 Chirality : 0.044 0.148 1399 Planarity : 0.004 0.040 1538 Dihedral : 5.717 63.103 1252 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.55 % Allowed : 18.19 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.08 (0.26), residues: 1112 helix: 2.34 (1.04), residues: 24 sheet: -0.12 (0.22), residues: 574 loop : 0.11 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 50 HIS 0.004 0.001 HIS B 353 PHE 0.021 0.001 PHE B 87 TYR 0.010 0.001 TYR A 238 ARG 0.008 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.973 Fit side-chains REVERT: A 321 TYR cc_start: 0.8644 (m-80) cc_final: 0.8326 (m-80) REVERT: H 22 ARG cc_start: 0.7589 (ttt90) cc_final: 0.7237 (ttt90) REVERT: H 33 TYR cc_start: 0.8458 (m-80) cc_final: 0.8150 (m-80) REVERT: H 41 ARG cc_start: 0.8747 (ptt-90) cc_final: 0.7928 (ptm160) REVERT: H 87 ASN cc_start: 0.7810 (m-40) cc_final: 0.7576 (m-40) REVERT: H 93 ASP cc_start: 0.6047 (m-30) cc_final: 0.5710 (m-30) REVERT: B 75 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7422 (p90) REVERT: B 242 CYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7988 (p) REVERT: B 314 ILE cc_start: 0.7903 (mm) cc_final: 0.7526 (mp) REVERT: B 321 TYR cc_start: 0.8465 (m-80) cc_final: 0.8096 (m-80) REVERT: I 33 TYR cc_start: 0.8569 (m-80) cc_final: 0.8158 (m-80) REVERT: I 41 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7942 (ptt180) REVERT: M 28 GLN cc_start: 0.7395 (mp10) cc_final: 0.7029 (mp10) outliers start: 33 outliers final: 25 residues processed: 145 average time/residue: 0.1875 time to fit residues: 38.7110 Evaluate side-chains 150 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain M residue 5 MET Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN B 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.140368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112595 restraints weight = 14662.790| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.01 r_work: 0.3356 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8917 Z= 0.283 Angle : 0.604 7.013 12146 Z= 0.308 Chirality : 0.045 0.145 1399 Planarity : 0.004 0.040 1538 Dihedral : 5.885 62.135 1252 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.12 % Allowed : 19.16 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.18 (0.26), residues: 1112 helix: 2.29 (1.03), residues: 24 sheet: -0.21 (0.22), residues: 574 loop : 0.06 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.005 0.001 HIS B 353 PHE 0.012 0.002 PHE L 99 TYR 0.014 0.002 TYR B 272 ARG 0.008 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.130 Fit side-chains REVERT: A 181 GLN cc_start: 0.8602 (tt0) cc_final: 0.8126 (tm-30) REVERT: A 321 TYR cc_start: 0.8604 (m-80) cc_final: 0.8305 (m-80) REVERT: H 33 TYR cc_start: 0.8566 (m-80) cc_final: 0.8168 (m-80) REVERT: H 87 ASN cc_start: 0.7873 (m-40) cc_final: 0.7625 (m-40) REVERT: H 93 ASP cc_start: 0.6133 (m-30) cc_final: 0.5770 (m-30) REVERT: L 82 GLU cc_start: 0.7777 (pm20) cc_final: 0.7417 (pm20) REVERT: B 75 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7778 (p90) REVERT: B 314 ILE cc_start: 0.7790 (mm) cc_final: 0.7392 (mp) REVERT: B 321 TYR cc_start: 0.8431 (m-80) cc_final: 0.8047 (m-80) REVERT: I 33 TYR cc_start: 0.8637 (m-80) cc_final: 0.8322 (m-80) REVERT: I 41 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8045 (ptt180) REVERT: I 89 LEU cc_start: 0.7919 (mm) cc_final: 0.7673 (mm) REVERT: M 28 GLN cc_start: 0.7200 (mp10) cc_final: 0.6807 (mp10) outliers start: 29 outliers final: 24 residues processed: 141 average time/residue: 0.2028 time to fit residues: 40.3895 Evaluate side-chains 150 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain M residue 5 MET Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 0.0050 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN L 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.141401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114160 restraints weight = 14430.535| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.98 r_work: 0.3383 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8917 Z= 0.212 Angle : 0.583 6.849 12146 Z= 0.297 Chirality : 0.044 0.148 1399 Planarity : 0.004 0.040 1538 Dihedral : 5.798 63.673 1252 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.69 % Allowed : 19.16 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.14 (0.26), residues: 1112 helix: 2.41 (1.04), residues: 24 sheet: -0.17 (0.22), residues: 574 loop : 0.07 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.004 0.001 HIS B 353 PHE 0.010 0.001 PHE B 268 TYR 0.011 0.001 TYR A 54 ARG 0.013 0.001 ARG B 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 181 GLN cc_start: 0.8537 (tt0) cc_final: 0.8163 (tm-30) REVERT: A 321 TYR cc_start: 0.8641 (m-80) cc_final: 0.8316 (m-80) REVERT: H 22 ARG cc_start: 0.7641 (ttt90) cc_final: 0.7291 (ttt90) REVERT: H 33 TYR cc_start: 0.8527 (m-80) cc_final: 0.8153 (m-80) REVERT: H 41 ARG cc_start: 0.8765 (ptt-90) cc_final: 0.7917 (ptm160) REVERT: H 87 ASN cc_start: 0.7841 (m-40) cc_final: 0.7592 (m-40) REVERT: H 93 ASP cc_start: 0.6059 (m-30) cc_final: 0.5695 (m-30) REVERT: L 82 GLU cc_start: 0.7762 (pm20) cc_final: 0.7384 (pm20) REVERT: B 75 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7654 (p90) REVERT: B 314 ILE cc_start: 0.7935 (mm) cc_final: 0.7644 (mp) REVERT: B 321 TYR cc_start: 0.8456 (m-80) cc_final: 0.8025 (m-80) REVERT: I 33 TYR cc_start: 0.8617 (m-80) cc_final: 0.8198 (m-80) REVERT: I 41 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7965 (ptt180) REVERT: M 28 GLN cc_start: 0.7282 (mp10) cc_final: 0.6906 (mp10) outliers start: 25 outliers final: 21 residues processed: 141 average time/residue: 0.2042 time to fit residues: 40.5030 Evaluate side-chains 148 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.141715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113509 restraints weight = 14570.426| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.13 r_work: 0.3364 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8917 Z= 0.220 Angle : 0.579 6.577 12146 Z= 0.295 Chirality : 0.044 0.146 1399 Planarity : 0.004 0.040 1538 Dihedral : 5.783 63.834 1252 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.80 % Allowed : 19.38 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.13 (0.26), residues: 1112 helix: 2.42 (1.05), residues: 24 sheet: -0.15 (0.22), residues: 574 loop : 0.06 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS B 353 PHE 0.010 0.001 PHE B 277 TYR 0.016 0.001 TYR L 37 ARG 0.009 0.000 ARG H 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3592.10 seconds wall clock time: 64 minutes 56.96 seconds (3896.96 seconds total)