Starting phenix.real_space_refine on Sat Sep 28 19:10:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/09_2024/6l3u_0826_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/09_2024/6l3u_0826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/09_2024/6l3u_0826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/09_2024/6l3u_0826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/09_2024/6l3u_0826_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/09_2024/6l3u_0826_trim.cif" } resolution = 2.53 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= 0.007 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 Ca 6 9.91 5 S 66 5.16 5 C 6540 2.51 5 N 1638 2.21 5 O 1860 1.98 5 H 9588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19698 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "B" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "C" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "D" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "E" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "F" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {' CA': 1, 'LMN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Time building chain proxies: 10.40, per 1000 atoms: 0.53 Number of scatterers: 19698 At special positions: 0 Unit cell: (119.121, 120.467, 92.874, 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) Ca 6 19.99 S 66 16.00 O 1860 8.00 N 1638 7.00 C 6540 6.00 H 9588 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.04 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.03 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: 4.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 78.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.043A pdb=" N LEU A 6 " --> pdb=" O CYS A 2 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 45 Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 107 Proline residue: A 87 - end of helix removed outlier: 3.531A pdb=" N HIS A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 105 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 214 removed outlier: 3.591A pdb=" N LEU A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.552A pdb=" N ARG B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 8 " --> pdb=" O ARG B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 23 through 45 Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 107 Proline residue: B 87 - end of helix removed outlier: 3.531A pdb=" N HIS B 102 " --> pdb=" O HIS B 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU B 105 " --> pdb=" O TRP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 214 removed outlier: 3.592A pdb=" N LEU B 210 " --> pdb=" O THR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.552A pdb=" N ARG C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 8 " --> pdb=" O ARG C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 23 through 45 Proline residue: C 41 - end of helix Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 107 Proline residue: C 87 - end of helix removed outlier: 3.531A pdb=" N HIS C 102 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 104 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU C 105 " --> pdb=" O TRP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.592A pdb=" N LEU C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'D' and resid 3 through 14 removed outlier: 3.552A pdb=" N ARG D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 23 through 45 Proline residue: D 41 - end of helix Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 107 Proline residue: D 87 - end of helix removed outlier: 3.532A pdb=" N HIS D 102 " --> pdb=" O HIS D 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU D 105 " --> pdb=" O TRP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 214 removed outlier: 3.591A pdb=" N LEU D 210 " --> pdb=" O THR D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'E' and resid 3 through 14 removed outlier: 3.552A pdb=" N ARG E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 8 " --> pdb=" O ARG E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 23 through 45 Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 107 Proline residue: E 87 - end of helix removed outlier: 3.532A pdb=" N HIS E 102 " --> pdb=" O HIS E 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 105 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 214 removed outlier: 3.591A pdb=" N LEU E 210 " --> pdb=" O THR E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'F' and resid 3 through 14 removed outlier: 3.552A pdb=" N ARG F 7 " --> pdb=" O GLY F 3 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG F 8 " --> pdb=" O ARG F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 23 through 45 Proline residue: F 41 - end of helix Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 107 Proline residue: F 87 - end of helix removed outlier: 3.531A pdb=" N HIS F 102 " --> pdb=" O HIS F 98 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU F 105 " --> pdb=" O TRP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 159 removed outlier: 3.978A pdb=" N ARG F 132 " --> pdb=" O ALA F 128 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU F 133 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU F 134 " --> pdb=" O SER F 130 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 214 removed outlier: 3.591A pdb=" N LEU F 210 " --> pdb=" O THR F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 219 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 53 690 hydrogen bonds defined for protein. 2052 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: 6.21 Time building geometry restraints manager: 5.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9576 1.03 - 1.23: 12 1.23 - 1.42: 4380 1.42 - 1.62: 5760 1.62 - 1.82: 84 Bond restraints: 19812 Sorted by residual: bond pdb=" CBS LMN C 301 " pdb=" CCM LMN C 301 " ideal model delta sigma weight residual 1.529 1.614 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CBS LMN A 303 " pdb=" CCM LMN A 303 " ideal model delta sigma weight residual 1.529 1.614 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CBS LMN E 301 " pdb=" CCM LMN E 301 " ideal model delta sigma weight residual 1.529 1.614 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CBS LMN D 301 " pdb=" CCM LMN D 301 " ideal model delta sigma weight residual 1.529 1.613 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" CBS LMN A 301 " pdb=" CCM LMN A 301 " ideal model delta sigma weight residual 1.529 1.613 -0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 19807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 33931 1.77 - 3.55: 1382 3.55 - 5.32: 208 5.32 - 7.10: 23 7.10 - 8.87: 6 Bond angle restraints: 35550 Sorted by residual: angle pdb=" N GLY E 45 " pdb=" CA GLY E 45 " pdb=" C GLY E 45 " ideal model delta sigma weight residual 112.73 117.03 -4.30 1.20e+00 6.94e-01 1.28e+01 angle pdb=" N GLY D 45 " pdb=" CA GLY D 45 " pdb=" C GLY D 45 " ideal model delta sigma weight residual 112.73 117.00 -4.27 1.20e+00 6.94e-01 1.27e+01 angle pdb=" N GLY B 45 " pdb=" CA GLY B 45 " pdb=" C GLY B 45 " ideal model delta sigma weight residual 112.73 117.00 -4.27 1.20e+00 6.94e-01 1.26e+01 angle pdb=" N GLY C 45 " pdb=" CA GLY C 45 " pdb=" C GLY C 45 " ideal model delta sigma weight residual 112.73 116.99 -4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" N GLY F 45 " pdb=" CA GLY F 45 " pdb=" C GLY F 45 " ideal model delta sigma weight residual 112.73 116.95 -4.22 1.20e+00 6.94e-01 1.23e+01 ... (remaining 35545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 8670 17.20 - 34.41: 750 34.41 - 51.61: 284 51.61 - 68.81: 142 68.81 - 86.01: 48 Dihedral angle restraints: 9894 sinusoidal: 5592 harmonic: 4302 Sorted by residual: dihedral pdb=" CAZ LMN A 303 " pdb=" CBB LMN A 303 " pdb=" CBD LMN A 303 " pdb=" CBF LMN A 303 " ideal model delta sinusoidal sigma weight residual 180.29 94.28 86.01 1 3.00e+01 1.11e-03 9.93e+00 dihedral pdb=" CAZ LMN E 301 " pdb=" CBB LMN E 301 " pdb=" CBD LMN E 301 " pdb=" CBF LMN E 301 " ideal model delta sinusoidal sigma weight residual 180.29 94.29 86.00 1 3.00e+01 1.11e-03 9.92e+00 dihedral pdb=" CAZ LMN A 301 " pdb=" CBB LMN A 301 " pdb=" CBD LMN A 301 " pdb=" CBF LMN A 301 " ideal model delta sinusoidal sigma weight residual 180.29 94.31 85.98 1 3.00e+01 1.11e-03 9.92e+00 ... (remaining 9891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1132 0.045 - 0.089: 352 0.089 - 0.134: 82 0.134 - 0.178: 6 0.178 - 0.223: 6 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CCV LMN D 301 " pdb=" CCR LMN D 301 " pdb=" CCT LMN D 301 " pdb=" OAU LMN D 301 " both_signs ideal model delta sigma weight residual False 2.28 2.50 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CCV LMN E 301 " pdb=" CCR LMN E 301 " pdb=" CCT LMN E 301 " pdb=" OAU LMN E 301 " both_signs ideal model delta sigma weight residual False 2.28 2.50 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CCV LMN A 301 " pdb=" CCR LMN A 301 " pdb=" CCT LMN A 301 " pdb=" OAU LMN A 301 " both_signs ideal model delta sigma weight residual False 2.28 2.50 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1575 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 25 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 26 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 25 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO E 26 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 26 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 26 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 25 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 26 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 26 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 26 " -0.023 5.00e-02 4.00e+02 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.28: 2775 2.28 - 2.86: 40450 2.86 - 3.44: 45782 3.44 - 4.02: 64892 4.02 - 4.60: 99365 Nonbonded interactions: 253264 Sorted by model distance: nonbonded pdb="HH11 ARG F 75 " pdb=" O HOH F 405 " model vdw 1.706 2.450 nonbonded pdb="HH11 ARG C 75 " pdb=" O HOH C 405 " model vdw 1.706 2.450 nonbonded pdb=" O CYS B 202 " pdb=" HG1 THR B 206 " model vdw 1.707 2.450 nonbonded pdb=" O CYS E 202 " pdb=" HG1 THR E 206 " model vdw 1.708 2.450 nonbonded pdb=" O CYS A 202 " pdb=" HG1 THR A 206 " model vdw 1.708 2.450 ... (remaining 253259 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 2 through 221) selection = (chain 'B' and resid 2 through 221) selection = (chain 'C' and resid 2 through 221) selection = (chain 'D' and resid 2 through 221) selection = (chain 'E' and resid 2 through 221) selection = (chain 'F' and resid 2 through 221) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.360 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 41.220 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.010 0.085 10224 Z= 0.679 Angle : 0.962 8.874 13872 Z= 0.425 Chirality : 0.047 0.223 1578 Planarity : 0.006 0.041 1650 Dihedral : 17.458 86.014 4194 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.01 % Allowed : 6.63 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.20), residues: 1182 helix: -1.90 (0.13), residues: 822 sheet: 0.71 (0.65), residues: 60 loop : -1.82 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 103 HIS 0.004 0.001 HIS D 98 PHE 0.013 0.002 PHE F 51 TYR 0.006 0.002 TYR D 156 ARG 0.004 0.001 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7010 (mtt-85) REVERT: A 50 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8072 (mt-10) REVERT: A 132 ARG cc_start: 0.7174 (ptp-170) cc_final: 0.6151 (tpm170) REVERT: B 16 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6938 (mtt-85) REVERT: B 50 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8366 (mt-10) REVERT: B 102 HIS cc_start: 0.7959 (m-70) cc_final: 0.7718 (m-70) REVERT: B 132 ARG cc_start: 0.7175 (ptp-170) cc_final: 0.6258 (tpm170) REVERT: B 135 TRP cc_start: 0.7514 (m-10) cc_final: 0.7122 (m100) REVERT: C 16 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6929 (mtt-85) REVERT: C 132 ARG cc_start: 0.7169 (ptp-170) cc_final: 0.6328 (tmt170) REVERT: C 135 TRP cc_start: 0.7492 (m-10) cc_final: 0.7177 (m100) REVERT: D 16 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7005 (mtt-85) REVERT: D 50 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8191 (mt-10) REVERT: D 132 ARG cc_start: 0.7149 (ptp-170) cc_final: 0.6125 (tpm170) REVERT: D 135 TRP cc_start: 0.7529 (m-10) cc_final: 0.7228 (m100) REVERT: E 16 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6920 (mtt-85) REVERT: E 50 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8369 (mt-10) REVERT: E 102 HIS cc_start: 0.7969 (m-70) cc_final: 0.7720 (m-70) REVERT: E 132 ARG cc_start: 0.7199 (ptp-170) cc_final: 0.6250 (tpm170) REVERT: E 135 TRP cc_start: 0.7530 (m-10) cc_final: 0.7157 (m100) REVERT: F 16 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6934 (mtt-85) REVERT: F 132 ARG cc_start: 0.7161 (ptp-170) cc_final: 0.6312 (tmt170) REVERT: F 135 TRP cc_start: 0.7503 (m-10) cc_final: 0.7191 (m100) outliers start: 30 outliers final: 6 residues processed: 178 average time/residue: 2.9313 time to fit residues: 554.7778 Evaluate side-chains 131 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 49 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B 80 GLN C 80 GLN D 80 GLN F 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10224 Z= 0.250 Angle : 0.661 4.743 13872 Z= 0.337 Chirality : 0.039 0.121 1578 Planarity : 0.007 0.033 1650 Dihedral : 12.788 81.545 2106 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.81 % Allowed : 11.04 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1182 helix: 0.95 (0.16), residues: 864 sheet: 0.59 (0.57), residues: 60 loop : -1.32 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 103 HIS 0.002 0.001 HIS A 54 PHE 0.013 0.002 PHE B 94 TYR 0.010 0.003 TYR E 159 ARG 0.003 0.001 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.561 Fit side-chains REVERT: A 16 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.6974 (mtt-85) REVERT: A 135 TRP cc_start: 0.7430 (m-10) cc_final: 0.7136 (m100) REVERT: A 220 ARG cc_start: 0.2586 (OUTLIER) cc_final: 0.1991 (tpm170) REVERT: B 16 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6934 (mtt-85) REVERT: B 135 TRP cc_start: 0.7384 (m-10) cc_final: 0.7131 (m100) REVERT: B 220 ARG cc_start: 0.2483 (OUTLIER) cc_final: 0.1830 (tpm170) REVERT: C 16 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6937 (mtt-85) REVERT: C 135 TRP cc_start: 0.7418 (m-10) cc_final: 0.7117 (m100) REVERT: C 220 ARG cc_start: 0.2617 (OUTLIER) cc_final: 0.1945 (tpm170) REVERT: D 16 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7022 (mtt-85) REVERT: D 135 TRP cc_start: 0.7398 (m-10) cc_final: 0.7105 (m100) REVERT: D 220 ARG cc_start: 0.2501 (OUTLIER) cc_final: 0.1925 (tpm170) REVERT: E 16 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6919 (mtt-85) REVERT: E 135 TRP cc_start: 0.7381 (m-10) cc_final: 0.7010 (m100) REVERT: E 220 ARG cc_start: 0.2532 (OUTLIER) cc_final: 0.1883 (tpm170) REVERT: F 16 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.6921 (mtt-85) REVERT: F 135 TRP cc_start: 0.7415 (m-10) cc_final: 0.7118 (m100) REVERT: F 220 ARG cc_start: 0.2612 (OUTLIER) cc_final: 0.1933 (tpm170) outliers start: 28 outliers final: 12 residues processed: 132 average time/residue: 3.7739 time to fit residues: 526.0980 Evaluate side-chains 132 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10224 Z= 0.187 Angle : 0.543 4.367 13872 Z= 0.278 Chirality : 0.035 0.113 1578 Planarity : 0.005 0.032 1650 Dihedral : 11.817 85.405 2106 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.21 % Allowed : 11.95 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.24), residues: 1182 helix: 2.16 (0.17), residues: 864 sheet: 0.98 (0.58), residues: 60 loop : -1.35 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 101 HIS 0.002 0.001 HIS E 54 PHE 0.011 0.001 PHE D 94 TYR 0.008 0.002 TYR D 97 ARG 0.007 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.616 Fit side-chains REVERT: A 16 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7029 (mtt-85) REVERT: A 135 TRP cc_start: 0.7365 (m-10) cc_final: 0.7075 (m100) REVERT: B 16 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6968 (mtt-85) REVERT: B 102 HIS cc_start: 0.7903 (m-70) cc_final: 0.7664 (m-70) REVERT: B 135 TRP cc_start: 0.7337 (m-10) cc_final: 0.7108 (m100) REVERT: C 16 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7023 (mtt-85) REVERT: C 102 HIS cc_start: 0.7893 (m-70) cc_final: 0.7691 (m-70) REVERT: C 135 TRP cc_start: 0.7419 (m-10) cc_final: 0.7142 (m100) REVERT: D 16 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7059 (mtt-85) REVERT: D 135 TRP cc_start: 0.7322 (m-10) cc_final: 0.7044 (m100) REVERT: E 16 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6965 (mtt-85) REVERT: E 102 HIS cc_start: 0.7916 (m-70) cc_final: 0.7676 (m-70) REVERT: E 135 TRP cc_start: 0.7356 (m-10) cc_final: 0.7121 (m100) REVERT: F 16 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7017 (mtt-85) REVERT: F 135 TRP cc_start: 0.7421 (m-10) cc_final: 0.7133 (m100) outliers start: 22 outliers final: 6 residues processed: 140 average time/residue: 3.3344 time to fit residues: 493.7437 Evaluate side-chains 130 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 49 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10224 Z= 0.202 Angle : 0.548 4.586 13872 Z= 0.277 Chirality : 0.035 0.112 1578 Planarity : 0.005 0.028 1650 Dihedral : 11.590 89.768 2106 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.31 % Allowed : 13.35 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.25), residues: 1182 helix: 2.42 (0.17), residues: 864 sheet: 1.18 (0.58), residues: 60 loop : -1.41 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 101 HIS 0.002 0.001 HIS E 54 PHE 0.012 0.002 PHE C 51 TYR 0.009 0.002 TYR F 156 ARG 0.002 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.705 Fit side-chains REVERT: A 16 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7170 (mtt-85) REVERT: A 135 TRP cc_start: 0.7403 (m-10) cc_final: 0.7123 (m100) REVERT: B 16 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7097 (mtt-85) REVERT: B 102 HIS cc_start: 0.7918 (m-70) cc_final: 0.7665 (m-70) REVERT: B 135 TRP cc_start: 0.7357 (m-10) cc_final: 0.7136 (m100) REVERT: C 135 TRP cc_start: 0.7415 (m-10) cc_final: 0.7155 (m100) REVERT: D 16 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7184 (mtt-85) REVERT: D 135 TRP cc_start: 0.7391 (m-10) cc_final: 0.7117 (m100) REVERT: E 16 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7176 (mtt-85) REVERT: E 102 HIS cc_start: 0.7910 (m-70) cc_final: 0.7685 (m-70) REVERT: E 135 TRP cc_start: 0.7358 (m-10) cc_final: 0.7126 (m100) REVERT: F 135 TRP cc_start: 0.7427 (m-10) cc_final: 0.7169 (m100) outliers start: 13 outliers final: 6 residues processed: 126 average time/residue: 3.5499 time to fit residues: 471.6973 Evaluate side-chains 123 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10224 Z= 0.144 Angle : 0.471 4.432 13872 Z= 0.242 Chirality : 0.033 0.115 1578 Planarity : 0.004 0.026 1650 Dihedral : 10.211 80.510 2092 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.20 % Allowed : 13.45 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.25), residues: 1182 helix: 2.74 (0.17), residues: 864 sheet: 1.57 (0.62), residues: 60 loop : -1.45 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 101 HIS 0.002 0.001 HIS D 54 PHE 0.009 0.001 PHE A 51 TYR 0.008 0.001 TYR F 156 ARG 0.002 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 TRP cc_start: 0.7391 (m-10) cc_final: 0.7126 (m100) REVERT: B 16 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7217 (mtt-85) REVERT: B 102 HIS cc_start: 0.7808 (m-70) cc_final: 0.7572 (m-70) REVERT: B 135 TRP cc_start: 0.7335 (m-10) cc_final: 0.7094 (m100) REVERT: C 135 TRP cc_start: 0.7403 (m-10) cc_final: 0.7141 (m100) REVERT: D 135 TRP cc_start: 0.7352 (m-10) cc_final: 0.7096 (m100) REVERT: E 16 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7180 (mtt-85) REVERT: E 102 HIS cc_start: 0.7815 (m-70) cc_final: 0.7585 (m-70) REVERT: E 135 TRP cc_start: 0.7346 (m-10) cc_final: 0.7101 (m100) REVERT: F 135 TRP cc_start: 0.7410 (m-10) cc_final: 0.7149 (m100) outliers start: 12 outliers final: 6 residues processed: 125 average time/residue: 3.4813 time to fit residues: 458.1868 Evaluate side-chains 121 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10224 Z= 0.184 Angle : 0.517 4.499 13872 Z= 0.261 Chirality : 0.035 0.132 1578 Planarity : 0.005 0.027 1650 Dihedral : 9.559 82.851 2084 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.80 % Allowed : 13.55 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.25), residues: 1182 helix: 2.75 (0.17), residues: 864 sheet: 1.75 (0.63), residues: 60 loop : -1.56 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 101 HIS 0.002 0.001 HIS A 54 PHE 0.011 0.001 PHE C 51 TYR 0.009 0.002 TYR D 97 ARG 0.001 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 TRP cc_start: 0.7405 (m-10) cc_final: 0.7148 (m100) REVERT: B 16 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7282 (mtt-85) REVERT: B 135 TRP cc_start: 0.7366 (m-10) cc_final: 0.7127 (m100) REVERT: C 135 TRP cc_start: 0.7442 (m-10) cc_final: 0.7159 (m100) REVERT: D 135 TRP cc_start: 0.7390 (m-10) cc_final: 0.7139 (m100) REVERT: E 16 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7213 (mtt-85) REVERT: E 135 TRP cc_start: 0.7350 (m-10) cc_final: 0.7115 (m100) REVERT: F 135 TRP cc_start: 0.7443 (m-10) cc_final: 0.7164 (m100) outliers start: 8 outliers final: 6 residues processed: 119 average time/residue: 3.6719 time to fit residues: 463.2250 Evaluate side-chains 117 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10224 Z= 0.253 Angle : 0.580 4.959 13872 Z= 0.294 Chirality : 0.037 0.131 1578 Planarity : 0.005 0.040 1650 Dihedral : 9.444 88.297 2084 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.80 % Allowed : 13.76 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.25), residues: 1182 helix: 2.53 (0.17), residues: 870 sheet: 1.65 (0.64), residues: 60 loop : -1.45 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 103 HIS 0.003 0.001 HIS E 98 PHE 0.015 0.002 PHE F 51 TYR 0.011 0.003 TYR B 159 ARG 0.002 0.000 ARG E 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.553 Fit side-chains REVERT: A 135 TRP cc_start: 0.7404 (m-10) cc_final: 0.7141 (m100) REVERT: B 16 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7239 (mtt-85) REVERT: B 135 TRP cc_start: 0.7370 (m-10) cc_final: 0.7018 (m100) REVERT: C 135 TRP cc_start: 0.7475 (m-10) cc_final: 0.7195 (m100) REVERT: D 135 TRP cc_start: 0.7407 (m-10) cc_final: 0.7146 (m100) REVERT: E 16 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7247 (mtt-85) REVERT: E 135 TRP cc_start: 0.7370 (m-10) cc_final: 0.7010 (m100) REVERT: F 135 TRP cc_start: 0.7473 (m-10) cc_final: 0.7194 (m100) outliers start: 8 outliers final: 6 residues processed: 119 average time/residue: 3.5575 time to fit residues: 446.0408 Evaluate side-chains 119 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10224 Z= 0.206 Angle : 0.533 4.789 13872 Z= 0.272 Chirality : 0.036 0.137 1578 Planarity : 0.005 0.041 1650 Dihedral : 8.947 87.185 2084 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.80 % Allowed : 13.96 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.25), residues: 1182 helix: 2.57 (0.17), residues: 870 sheet: 1.77 (0.64), residues: 60 loop : -1.43 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 103 HIS 0.003 0.001 HIS C 54 PHE 0.012 0.002 PHE F 51 TYR 0.010 0.002 TYR D 97 ARG 0.003 0.000 ARG E 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.590 Fit side-chains REVERT: A 135 TRP cc_start: 0.7393 (m-10) cc_final: 0.7131 (m100) REVERT: B 16 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7732 (mtt90) REVERT: B 135 TRP cc_start: 0.7374 (m-10) cc_final: 0.7031 (m100) REVERT: C 135 TRP cc_start: 0.7456 (m-10) cc_final: 0.7186 (m100) REVERT: D 135 TRP cc_start: 0.7382 (m-10) cc_final: 0.7131 (m100) REVERT: E 16 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7732 (mtt90) REVERT: E 135 TRP cc_start: 0.7353 (m-10) cc_final: 0.7001 (m100) REVERT: F 135 TRP cc_start: 0.7454 (m-10) cc_final: 0.7183 (m100) outliers start: 8 outliers final: 6 residues processed: 119 average time/residue: 3.5468 time to fit residues: 444.8157 Evaluate side-chains 119 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10224 Z= 0.196 Angle : 0.531 4.675 13872 Z= 0.269 Chirality : 0.035 0.142 1578 Planarity : 0.005 0.059 1650 Dihedral : 8.578 82.178 2084 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.00 % Allowed : 13.86 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.25), residues: 1182 helix: 2.63 (0.17), residues: 870 sheet: 1.75 (0.64), residues: 60 loop : -1.41 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 103 HIS 0.002 0.001 HIS E 102 PHE 0.013 0.002 PHE F 51 TYR 0.010 0.002 TYR A 156 ARG 0.002 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.476 Fit side-chains REVERT: A 135 TRP cc_start: 0.7389 (m-10) cc_final: 0.7129 (m100) REVERT: B 16 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7724 (mtt90) REVERT: B 135 TRP cc_start: 0.7355 (m-10) cc_final: 0.7001 (m100) REVERT: C 135 TRP cc_start: 0.7463 (m-10) cc_final: 0.7156 (m100) REVERT: D 135 TRP cc_start: 0.7389 (m-10) cc_final: 0.7131 (m100) REVERT: E 16 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7731 (mtt90) REVERT: E 135 TRP cc_start: 0.7358 (m-10) cc_final: 0.7003 (m100) REVERT: F 135 TRP cc_start: 0.7460 (m-10) cc_final: 0.7152 (m100) outliers start: 10 outliers final: 6 residues processed: 121 average time/residue: 3.4927 time to fit residues: 445.8510 Evaluate side-chains 119 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 95 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10224 Z= 0.215 Angle : 0.543 4.779 13872 Z= 0.275 Chirality : 0.036 0.138 1578 Planarity : 0.005 0.039 1650 Dihedral : 8.571 76.202 2084 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.60 % Allowed : 14.76 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.24), residues: 1182 helix: 2.67 (0.17), residues: 864 sheet: 1.78 (0.64), residues: 60 loop : -1.49 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 103 HIS 0.002 0.001 HIS B 102 PHE 0.013 0.002 PHE C 51 TYR 0.010 0.002 TYR A 97 ARG 0.002 0.000 ARG E 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.507 Fit side-chains REVERT: A 135 TRP cc_start: 0.7394 (m-10) cc_final: 0.7139 (m100) REVERT: B 135 TRP cc_start: 0.7384 (m-10) cc_final: 0.7039 (m100) REVERT: C 135 TRP cc_start: 0.7465 (m-10) cc_final: 0.7157 (m100) REVERT: D 135 TRP cc_start: 0.7390 (m-10) cc_final: 0.7131 (m100) REVERT: E 135 TRP cc_start: 0.7383 (m-10) cc_final: 0.7040 (m100) REVERT: F 135 TRP cc_start: 0.7466 (m-10) cc_final: 0.7157 (m100) outliers start: 6 outliers final: 6 residues processed: 117 average time/residue: 3.6533 time to fit residues: 453.7047 Evaluate side-chains 117 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.156971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118058 restraints weight = 25582.219| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.37 r_work: 0.3066 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10224 Z= 0.141 Angle : 0.476 4.418 13872 Z= 0.242 Chirality : 0.034 0.145 1578 Planarity : 0.005 0.064 1650 Dihedral : 7.608 65.268 2076 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.60 % Allowed : 14.56 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.25), residues: 1182 helix: 2.87 (0.17), residues: 864 sheet: 1.78 (0.65), residues: 60 loop : -1.51 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 101 HIS 0.002 0.001 HIS C 69 PHE 0.007 0.001 PHE C 51 TYR 0.008 0.001 TYR F 156 ARG 0.001 0.000 ARG C 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8054.06 seconds wall clock time: 138 minutes 55.43 seconds (8335.43 seconds total)