Starting phenix.real_space_refine on Fri Feb 16 12:35:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rld_4919/02_2024/6rld_4919_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rld_4919/02_2024/6rld_4919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rld_4919/02_2024/6rld_4919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rld_4919/02_2024/6rld_4919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rld_4919/02_2024/6rld_4919_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rld_4919/02_2024/6rld_4919_updated.pdb" } resolution = 2.9 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= 0.008 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 21 5.49 5 S 42 5.16 5 C 10045 2.51 5 N 2492 2.21 5 O 2709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F ARG 256": "NH1" <-> "NH2" Residue "G ARG 74": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G ARG 256": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15309 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "B" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "C" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "D" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "E" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "F" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "G" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.20, per 1000 atoms: 0.54 Number of scatterers: 15309 At special positions: 0 Unit cell: (97.842, 98.9055, 145.7, 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 42 16.00 P 21 15.00 O 2709 8.00 N 2492 7.00 C 10045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.89 Conformation dependent library (CDL) restraints added in 2.8 seconds 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 14 sheets defined 49.4% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 23 through 57 Processing helix chain 'A' and resid 63 through 89 Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 246 through 263 Processing helix chain 'B' and resid 23 through 57 Processing helix chain 'B' and resid 63 through 89 Processing helix chain 'B' and resid 94 through 110 Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 246 through 263 Processing helix chain 'C' and resid 23 through 57 Processing helix chain 'C' and resid 63 through 89 Processing helix chain 'C' and resid 94 through 110 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 246 through 263 Processing helix chain 'D' and resid 23 through 57 Processing helix chain 'D' and resid 63 through 89 Processing helix chain 'D' and resid 94 through 110 Processing helix chain 'D' and resid 112 through 126 Processing helix chain 'D' and resid 167 through 172 removed outlier: 3.557A pdb=" N ALA D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 246 through 263 Processing helix chain 'E' and resid 23 through 57 Processing helix chain 'E' and resid 63 through 89 Processing helix chain 'E' and resid 94 through 110 Processing helix chain 'E' and resid 112 through 126 Processing helix chain 'E' and resid 167 through 172 removed outlier: 3.557A pdb=" N ALA E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 246 through 263 Processing helix chain 'F' and resid 23 through 57 Processing helix chain 'F' and resid 63 through 89 Processing helix chain 'F' and resid 94 through 110 Processing helix chain 'F' and resid 112 through 126 Processing helix chain 'F' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 210 Processing helix chain 'F' and resid 246 through 263 Processing helix chain 'G' and resid 23 through 57 Processing helix chain 'G' and resid 63 through 89 Processing helix chain 'G' and resid 94 through 110 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 210 Processing helix chain 'G' and resid 246 through 263 Processing sheet with id= A, first strand: chain 'A' and resid 175 through 177 removed outlier: 6.925A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N TRP A 240 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET A 221 " --> pdb=" O TRP A 240 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.925A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.925A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 175 through 177 removed outlier: 6.925A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 175 through 177 removed outlier: 6.925A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 175 through 177 removed outlier: 6.925A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 175 through 177 removed outlier: 6.925A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.141A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP G 240 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET G 221 " --> pdb=" O TRP G 240 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2604 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: 4.16 Time building geometry restraints manager: 6.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2359 1.31 - 1.43: 3688 1.43 - 1.56: 9291 1.56 - 1.68: 55 1.68 - 1.81: 84 Bond restraints: 15477 Sorted by residual: bond pdb=" C11 PCW F 602 " pdb=" O3 PCW F 602 " ideal model delta sigma weight residual 1.326 1.400 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C11 PCW G 602 " pdb=" O3 PCW G 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C11 PCW B 602 " pdb=" O3 PCW B 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C11 PCW E 602 " pdb=" O3 PCW E 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C11 PCW A 602 " pdb=" O3 PCW A 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 15472 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.98: 273 106.98 - 113.76: 9382 113.76 - 120.53: 5992 120.53 - 127.31: 5052 127.31 - 134.09: 77 Bond angle restraints: 20776 Sorted by residual: angle pdb=" O3P PCW D 603 " pdb=" P PCW D 603 " pdb=" O4P PCW D 603 " ideal model delta sigma weight residual 96.85 110.12 -13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" O3P PCW E 603 " pdb=" P PCW E 603 " pdb=" O4P PCW E 603 " ideal model delta sigma weight residual 96.85 110.09 -13.24 3.00e+00 1.11e-01 1.95e+01 angle pdb=" O3P PCW B 603 " pdb=" P PCW B 603 " pdb=" O4P PCW B 603 " ideal model delta sigma weight residual 96.85 110.08 -13.23 3.00e+00 1.11e-01 1.95e+01 angle pdb=" O3P PCW F 603 " pdb=" P PCW F 603 " pdb=" O4P PCW F 603 " ideal model delta sigma weight residual 96.85 110.08 -13.23 3.00e+00 1.11e-01 1.95e+01 angle pdb=" O3P PCW G 603 " pdb=" P PCW G 603 " pdb=" O4P PCW G 603 " ideal model delta sigma weight residual 96.85 110.08 -13.23 3.00e+00 1.11e-01 1.94e+01 ... (remaining 20771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.01: 9100 32.01 - 64.02: 399 64.02 - 96.03: 21 96.03 - 128.05: 21 128.05 - 160.06: 14 Dihedral angle restraints: 9555 sinusoidal: 4235 harmonic: 5320 Sorted by residual: dihedral pdb=" CA ILE E 61 " pdb=" C ILE E 61 " pdb=" N ASP E 62 " pdb=" CA ASP E 62 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ILE G 61 " pdb=" C ILE G 61 " pdb=" N ASP G 62 " pdb=" CA ASP G 62 " ideal model delta harmonic sigma weight residual 180.00 150.05 29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ILE A 61 " pdb=" C ILE A 61 " pdb=" N ASP A 62 " pdb=" CA ASP A 62 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 9552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1520 0.045 - 0.089: 643 0.089 - 0.134: 158 0.134 - 0.179: 49 0.179 - 0.224: 45 Chirality restraints: 2415 Sorted by residual: chirality pdb=" C2 PCW G 601 " pdb=" C1 PCW G 601 " pdb=" C3 PCW G 601 " pdb=" O2 PCW G 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C2 PCW D 601 " pdb=" C1 PCW D 601 " pdb=" C3 PCW D 601 " pdb=" O2 PCW D 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C2 PCW C 601 " pdb=" C1 PCW C 601 " pdb=" C3 PCW C 601 " pdb=" O2 PCW C 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2412 not shown) Planarity restraints: 2548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 270 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO D 271 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 271 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 271 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 270 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO G 271 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO G 271 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 271 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 270 " 0.047 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO C 271 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 271 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 271 " 0.039 5.00e-02 4.00e+02 ... (remaining 2545 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 4183 2.82 - 3.34: 13300 3.34 - 3.86: 25065 3.86 - 4.38: 27457 4.38 - 4.90: 49801 Nonbonded interactions: 119806 Sorted by model distance: nonbonded pdb=" NH2 ARG D 224 " pdb=" OD1 ASP E 252 " model vdw 2.306 2.520 nonbonded pdb=" NH2 ARG E 224 " pdb=" OD1 ASP F 252 " model vdw 2.326 2.520 nonbonded pdb=" NE2 GLN A 272 " pdb=" OD2 ASP G 274 " model vdw 2.330 2.520 nonbonded pdb=" NH2 ARG B 224 " pdb=" OD1 ASP C 252 " model vdw 2.350 2.520 nonbonded pdb=" NH2 ARG F 224 " pdb=" OD1 ASP G 252 " model vdw 2.357 2.520 ... (remaining 119801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.260 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 41.880 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.009 0.087 15477 Z= 0.587 Angle : 1.376 13.269 20776 Z= 0.602 Chirality : 0.059 0.224 2415 Planarity : 0.006 0.071 2548 Dihedral : 18.759 160.058 6125 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.47 % Allowed : 3.72 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.15), residues: 1841 helix: -2.06 (0.12), residues: 987 sheet: -1.77 (0.24), residues: 308 loop : -2.40 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 251 PHE 0.040 0.005 PHE C 235 TYR 0.035 0.004 TYR D 75 ARG 0.005 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 322 time to evaluate : 1.652 Fit side-chains REVERT: A 35 LEU cc_start: 0.8480 (mt) cc_final: 0.8165 (mp) REVERT: A 47 MET cc_start: 0.6802 (mmp) cc_final: 0.6016 (tmm) REVERT: B 227 GLU cc_start: 0.8054 (tt0) cc_final: 0.7779 (tt0) REVERT: C 47 MET cc_start: 0.6811 (mmp) cc_final: 0.6305 (tmm) REVERT: C 273 MET cc_start: 0.8123 (ttm) cc_final: 0.7918 (ttp) REVERT: D 47 MET cc_start: 0.6751 (mmp) cc_final: 0.6133 (tmm) REVERT: D 278 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8136 (mtpt) REVERT: E 47 MET cc_start: 0.6967 (mmp) cc_final: 0.6318 (tmm) REVERT: E 227 GLU cc_start: 0.8119 (tt0) cc_final: 0.7860 (tt0) REVERT: F 47 MET cc_start: 0.7138 (mmp) cc_final: 0.6509 (tmm) REVERT: F 92 GLN cc_start: 0.8455 (tt0) cc_final: 0.8163 (tt0) REVERT: F 149 GLN cc_start: 0.8214 (mt0) cc_final: 0.7998 (mt0) REVERT: G 47 MET cc_start: 0.6976 (mmp) cc_final: 0.6401 (tmm) REVERT: G 135 TYR cc_start: 0.8504 (t80) cc_final: 0.8220 (t80) REVERT: G 247 GLN cc_start: 0.8321 (tp40) cc_final: 0.8064 (tp-100) outliers start: 7 outliers final: 2 residues processed: 322 average time/residue: 1.5065 time to fit residues: 526.2945 Evaluate side-chains 192 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain B residue 68 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.3980 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 93 optimal weight: 0.0170 chunk 73 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 149 GLN B 149 GLN C 50 ASN C 92 GLN C 149 GLN D 50 ASN D 92 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN G 92 GLN G 149 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15477 Z= 0.155 Angle : 0.511 8.130 20776 Z= 0.265 Chirality : 0.042 0.131 2415 Planarity : 0.005 0.065 2548 Dihedral : 20.372 142.611 2967 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.06 % Allowed : 12.49 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 1841 helix: 0.28 (0.15), residues: 994 sheet: -1.39 (0.26), residues: 294 loop : -2.16 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 251 PHE 0.034 0.002 PHE D 68 TYR 0.007 0.001 TYR G 75 ARG 0.007 0.000 ARG D 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 253 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6533 (mmp) cc_final: 0.5970 (tmm) REVERT: A 60 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6991 (ptpp) REVERT: B 187 GLU cc_start: 0.8115 (tt0) cc_final: 0.7626 (tt0) REVERT: B 227 GLU cc_start: 0.8084 (tt0) cc_final: 0.7858 (tt0) REVERT: B 277 PHE cc_start: 0.7325 (t80) cc_final: 0.6852 (t80) REVERT: B 278 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8013 (mttt) REVERT: C 47 MET cc_start: 0.6610 (mmp) cc_final: 0.6252 (tmm) REVERT: C 273 MET cc_start: 0.8063 (ttm) cc_final: 0.7837 (ttp) REVERT: C 277 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: D 47 MET cc_start: 0.6627 (mmp) cc_final: 0.6180 (tmm) REVERT: D 210 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: E 47 MET cc_start: 0.6675 (mmp) cc_final: 0.6289 (tmm) REVERT: E 210 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: E 227 GLU cc_start: 0.8062 (tt0) cc_final: 0.7716 (tt0) REVERT: F 47 MET cc_start: 0.6685 (mmp) cc_final: 0.6393 (tmm) REVERT: F 92 GLN cc_start: 0.8393 (tt0) cc_final: 0.8071 (tt0) REVERT: F 227 GLU cc_start: 0.7999 (tt0) cc_final: 0.7726 (tt0) REVERT: G 47 MET cc_start: 0.6833 (mmp) cc_final: 0.6331 (tmm) REVERT: G 72 LEU cc_start: 0.7538 (tp) cc_final: 0.7329 (tt) REVERT: G 135 TYR cc_start: 0.8560 (t80) cc_final: 0.8255 (t80) REVERT: G 221 MET cc_start: 0.8581 (mtm) cc_final: 0.8369 (mtm) outliers start: 46 outliers final: 8 residues processed: 284 average time/residue: 1.2502 time to fit residues: 391.1784 Evaluate side-chains 217 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 205 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 237 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 149 GLN A 210 GLN B 53 ASN B 92 GLN C 92 GLN C 149 GLN D 92 GLN E 92 GLN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15477 Z= 0.187 Angle : 0.480 8.227 20776 Z= 0.252 Chirality : 0.041 0.131 2415 Planarity : 0.004 0.057 2548 Dihedral : 19.160 149.635 2961 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.39 % Allowed : 16.94 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1841 helix: 1.25 (0.16), residues: 994 sheet: -0.91 (0.27), residues: 294 loop : -1.87 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 240 PHE 0.029 0.002 PHE A 68 TYR 0.008 0.001 TYR B 75 ARG 0.004 0.000 ARG D 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 221 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6540 (mmp) cc_final: 0.5961 (tmt) REVERT: A 60 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.7029 (ptpp) REVERT: A 153 THR cc_start: 0.9497 (p) cc_final: 0.9282 (t) REVERT: B 161 LYS cc_start: 0.8828 (ptpt) cc_final: 0.8557 (ptmt) REVERT: B 181 GLU cc_start: 0.7519 (tt0) cc_final: 0.7296 (tt0) REVERT: B 187 GLU cc_start: 0.8132 (tt0) cc_final: 0.7716 (tt0) REVERT: B 227 GLU cc_start: 0.8102 (tt0) cc_final: 0.7865 (tt0) REVERT: B 277 PHE cc_start: 0.7370 (t80) cc_final: 0.6834 (t80) REVERT: B 278 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8041 (mttt) REVERT: C 47 MET cc_start: 0.6672 (mmp) cc_final: 0.6185 (tmm) REVERT: C 273 MET cc_start: 0.8006 (ttm) cc_final: 0.7802 (ttp) REVERT: C 277 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: D 47 MET cc_start: 0.6557 (mmp) cc_final: 0.6073 (tmm) REVERT: D 169 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8927 (ttmm) REVERT: D 187 GLU cc_start: 0.8258 (tt0) cc_final: 0.8026 (tt0) REVERT: D 210 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: E 47 MET cc_start: 0.6598 (mmp) cc_final: 0.6220 (tmm) REVERT: E 210 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: E 227 GLU cc_start: 0.8058 (tt0) cc_final: 0.7727 (tt0) REVERT: F 47 MET cc_start: 0.6711 (mmp) cc_final: 0.6282 (tmm) REVERT: F 92 GLN cc_start: 0.8403 (tt0) cc_final: 0.8098 (tt0) REVERT: F 153 THR cc_start: 0.9406 (p) cc_final: 0.9192 (t) REVERT: F 227 GLU cc_start: 0.8025 (tt0) cc_final: 0.7754 (tt0) REVERT: G 47 MET cc_start: 0.6839 (mmp) cc_final: 0.6346 (tmm) REVERT: G 72 LEU cc_start: 0.7543 (tp) cc_final: 0.7291 (tt) REVERT: G 135 TYR cc_start: 0.8584 (t80) cc_final: 0.8278 (t80) outliers start: 51 outliers final: 15 residues processed: 253 average time/residue: 1.3442 time to fit residues: 373.0810 Evaluate side-chains 228 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.0170 chunk 124 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 47 optimal weight: 0.0370 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 149 GLN B 149 GLN C 53 ASN C 92 GLN C 149 GLN D 92 GLN E 92 GLN E 149 GLN G 149 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15477 Z= 0.144 Angle : 0.450 9.154 20776 Z= 0.234 Chirality : 0.040 0.134 2415 Planarity : 0.004 0.057 2548 Dihedral : 18.321 153.636 2961 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.12 % Allowed : 16.94 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1841 helix: 1.82 (0.16), residues: 987 sheet: -0.59 (0.27), residues: 294 loop : -1.58 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 16 PHE 0.024 0.001 PHE A 68 TYR 0.005 0.001 TYR G 75 ARG 0.003 0.000 ARG D 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 230 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6503 (mmp) cc_final: 0.5960 (tmt) REVERT: A 60 LYS cc_start: 0.7257 (ptmm) cc_final: 0.7040 (ptpp) REVERT: A 181 GLU cc_start: 0.8043 (tp30) cc_final: 0.7735 (tt0) REVERT: B 68 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.6124 (OUTLIER) REVERT: B 159 ASP cc_start: 0.7813 (t0) cc_final: 0.7611 (t0) REVERT: B 171 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8677 (mp) REVERT: B 181 GLU cc_start: 0.7526 (tt0) cc_final: 0.7232 (tt0) REVERT: B 187 GLU cc_start: 0.8159 (tt0) cc_final: 0.7824 (tt0) REVERT: B 220 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: B 227 GLU cc_start: 0.8113 (tt0) cc_final: 0.7910 (tt0) REVERT: B 277 PHE cc_start: 0.7378 (t80) cc_final: 0.6886 (t80) REVERT: C 47 MET cc_start: 0.6692 (mmp) cc_final: 0.6204 (tmm) REVERT: C 97 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8223 (mp) REVERT: C 155 MET cc_start: 0.8763 (ptt) cc_final: 0.8407 (ptt) REVERT: C 273 MET cc_start: 0.8036 (ttm) cc_final: 0.7703 (ttp) REVERT: C 277 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: D 35 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8308 (mp) REVERT: D 47 MET cc_start: 0.6576 (mmp) cc_final: 0.6061 (tmm) REVERT: D 187 GLU cc_start: 0.8231 (tt0) cc_final: 0.8028 (tt0) REVERT: D 210 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: D 253 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8226 (t) REVERT: E 47 MET cc_start: 0.6617 (mmp) cc_final: 0.6252 (tmt) REVERT: E 181 GLU cc_start: 0.8109 (tp30) cc_final: 0.7735 (tt0) REVERT: E 210 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: E 227 GLU cc_start: 0.8033 (tt0) cc_final: 0.7720 (tt0) REVERT: F 47 MET cc_start: 0.6698 (mmp) cc_final: 0.6309 (tmm) REVERT: F 92 GLN cc_start: 0.8231 (tt0) cc_final: 0.7893 (tt0) REVERT: F 105 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8098 (tt) REVERT: F 210 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: F 253 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8172 (t) REVERT: G 47 MET cc_start: 0.6808 (mmp) cc_final: 0.6404 (tmm) REVERT: G 72 LEU cc_start: 0.7577 (tp) cc_final: 0.7290 (tt) REVERT: G 135 TYR cc_start: 0.8590 (t80) cc_final: 0.8316 (t80) REVERT: G 278 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8161 (mtmt) outliers start: 62 outliers final: 18 residues processed: 274 average time/residue: 1.2494 time to fit residues: 376.8747 Evaluate side-chains 237 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 208 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 92 GLN A 149 GLN B 149 GLN C 92 GLN C 149 GLN E 92 GLN E 149 GLN G 210 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15477 Z= 0.329 Angle : 0.516 9.218 20776 Z= 0.271 Chirality : 0.042 0.170 2415 Planarity : 0.004 0.057 2548 Dihedral : 18.387 156.303 2961 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.45 % Allowed : 18.27 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 1841 helix: 1.89 (0.16), residues: 994 sheet: -0.35 (0.27), residues: 308 loop : -1.28 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 240 PHE 0.023 0.002 PHE A 68 TYR 0.009 0.001 TYR E 27 ARG 0.003 0.000 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 204 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6490 (mmp) cc_final: 0.5943 (tmt) REVERT: A 56 MET cc_start: 0.0926 (ptt) cc_final: 0.0724 (ptt) REVERT: A 149 GLN cc_start: 0.8059 (mt0) cc_final: 0.7721 (mm110) REVERT: B 68 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.6034 (OUTLIER) REVERT: B 149 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7931 (mm110) REVERT: B 159 ASP cc_start: 0.7929 (t0) cc_final: 0.7695 (t0) REVERT: B 171 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8713 (mp) REVERT: B 181 GLU cc_start: 0.7510 (tt0) cc_final: 0.7286 (tt0) REVERT: B 187 GLU cc_start: 0.8147 (tt0) cc_final: 0.7896 (tt0) REVERT: B 220 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: B 227 GLU cc_start: 0.8111 (tt0) cc_final: 0.7887 (tt0) REVERT: B 253 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8209 (t) REVERT: C 47 MET cc_start: 0.6682 (mmp) cc_final: 0.6098 (tmt) REVERT: C 155 MET cc_start: 0.8792 (ptt) cc_final: 0.8449 (ptt) REVERT: C 181 GLU cc_start: 0.8105 (tp30) cc_final: 0.7405 (mp0) REVERT: C 273 MET cc_start: 0.8042 (ttm) cc_final: 0.7747 (ttp) REVERT: D 35 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8296 (mp) REVERT: D 47 MET cc_start: 0.6605 (mmp) cc_final: 0.6030 (tmm) REVERT: D 210 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: E 47 MET cc_start: 0.6642 (mmp) cc_final: 0.6244 (tmt) REVERT: E 210 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: E 227 GLU cc_start: 0.8106 (tt0) cc_final: 0.7775 (tt0) REVERT: F 47 MET cc_start: 0.6807 (mmp) cc_final: 0.6359 (tmm) REVERT: F 92 GLN cc_start: 0.8425 (tt0) cc_final: 0.8148 (tt0) REVERT: F 105 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8126 (tt) REVERT: F 134 GLU cc_start: 0.8317 (tt0) cc_final: 0.8110 (tt0) REVERT: F 210 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: F 227 GLU cc_start: 0.8101 (tt0) cc_final: 0.7778 (tt0) REVERT: G 47 MET cc_start: 0.6745 (mmp) cc_final: 0.6300 (tmm) REVERT: G 60 LYS cc_start: 0.7587 (ptmm) cc_final: 0.7291 (ptpp) REVERT: G 72 LEU cc_start: 0.7589 (tp) cc_final: 0.7302 (tt) REVERT: G 135 TYR cc_start: 0.8563 (t80) cc_final: 0.8330 (t80) REVERT: G 247 GLN cc_start: 0.8377 (tp40) cc_final: 0.8175 (tp-100) outliers start: 67 outliers final: 22 residues processed: 254 average time/residue: 1.2544 time to fit residues: 351.2497 Evaluate side-chains 227 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN C 92 GLN C 149 GLN E 92 GLN E 149 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15477 Z= 0.194 Angle : 0.467 8.691 20776 Z= 0.243 Chirality : 0.040 0.128 2415 Planarity : 0.004 0.059 2548 Dihedral : 17.903 158.092 2961 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.39 % Allowed : 19.53 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 1841 helix: 2.15 (0.16), residues: 994 sheet: -0.22 (0.27), residues: 308 loop : -1.16 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 16 PHE 0.019 0.002 PHE E 68 TYR 0.007 0.001 TYR E 27 ARG 0.002 0.000 ARG D 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 214 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6478 (mmp) cc_final: 0.5946 (tmt) REVERT: A 149 GLN cc_start: 0.8098 (mt0) cc_final: 0.7759 (mm110) REVERT: A 181 GLU cc_start: 0.8037 (tp30) cc_final: 0.7694 (tt0) REVERT: B 47 MET cc_start: 0.6907 (mmp) cc_final: 0.6400 (tmm) REVERT: B 68 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.6176 (p90) REVERT: B 159 ASP cc_start: 0.7858 (t0) cc_final: 0.7629 (t0) REVERT: B 171 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8676 (mp) REVERT: B 181 GLU cc_start: 0.7495 (tt0) cc_final: 0.7193 (tt0) REVERT: B 187 GLU cc_start: 0.8160 (tt0) cc_final: 0.7923 (tt0) REVERT: B 220 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8084 (pt0) REVERT: B 227 GLU cc_start: 0.8101 (tt0) cc_final: 0.7887 (tt0) REVERT: B 253 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8188 (t) REVERT: B 278 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8123 (mtpt) REVERT: C 47 MET cc_start: 0.6639 (mmp) cc_final: 0.6031 (tmt) REVERT: C 155 MET cc_start: 0.8764 (ptt) cc_final: 0.8429 (ptt) REVERT: C 273 MET cc_start: 0.8030 (ttm) cc_final: 0.7737 (ttp) REVERT: D 47 MET cc_start: 0.6710 (mmp) cc_final: 0.6249 (tmm) REVERT: D 181 GLU cc_start: 0.8035 (tp30) cc_final: 0.7549 (mp0) REVERT: D 210 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: E 47 MET cc_start: 0.6496 (mmp) cc_final: 0.6159 (tmt) REVERT: E 181 GLU cc_start: 0.8072 (tp30) cc_final: 0.7614 (tt0) REVERT: E 210 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: E 227 GLU cc_start: 0.8089 (tt0) cc_final: 0.7765 (tt0) REVERT: F 47 MET cc_start: 0.6972 (mmp) cc_final: 0.6383 (tmm) REVERT: F 92 GLN cc_start: 0.8346 (tt0) cc_final: 0.8011 (tt0) REVERT: F 105 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8096 (tt) REVERT: F 134 GLU cc_start: 0.8269 (tt0) cc_final: 0.8033 (tt0) REVERT: F 155 MET cc_start: 0.8407 (ptt) cc_final: 0.7981 (ptm) REVERT: F 210 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: G 47 MET cc_start: 0.6753 (mmp) cc_final: 0.6305 (tmm) REVERT: G 60 LYS cc_start: 0.7524 (ptmm) cc_final: 0.7240 (ptpp) REVERT: G 72 LEU cc_start: 0.7552 (tp) cc_final: 0.7320 (tt) REVERT: G 134 GLU cc_start: 0.8232 (tt0) cc_final: 0.7950 (tt0) REVERT: G 135 TYR cc_start: 0.8561 (t80) cc_final: 0.8340 (t80) REVERT: G 149 GLN cc_start: 0.8270 (mt0) cc_final: 0.7894 (mm110) REVERT: G 181 GLU cc_start: 0.8034 (tp30) cc_final: 0.7542 (mp0) REVERT: G 247 GLN cc_start: 0.8321 (tp40) cc_final: 0.8086 (tp-100) REVERT: G 278 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8254 (mtmt) outliers start: 51 outliers final: 17 residues processed: 248 average time/residue: 1.3228 time to fit residues: 359.6760 Evaluate side-chains 221 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 203 GLN B 92 GLN C 92 GLN C 149 GLN E 92 GLN E 149 GLN E 207 ASN F 53 ASN G 210 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15477 Z= 0.165 Angle : 0.460 8.932 20776 Z= 0.237 Chirality : 0.040 0.131 2415 Planarity : 0.003 0.055 2548 Dihedral : 17.370 160.868 2961 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.19 % Allowed : 20.40 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 1841 helix: 2.31 (0.16), residues: 994 sheet: -0.12 (0.28), residues: 308 loop : -1.02 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 16 PHE 0.017 0.002 PHE E 68 TYR 0.015 0.001 TYR F 27 ARG 0.005 0.000 ARG D 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 204 time to evaluate : 1.667 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6462 (mmp) cc_final: 0.5947 (tmt) REVERT: A 181 GLU cc_start: 0.8017 (tp30) cc_final: 0.7541 (tt0) REVERT: B 47 MET cc_start: 0.6853 (mmp) cc_final: 0.6400 (tmm) REVERT: B 68 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.6280 (p90) REVERT: B 159 ASP cc_start: 0.7861 (t0) cc_final: 0.7636 (t0) REVERT: B 171 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8697 (mp) REVERT: B 181 GLU cc_start: 0.7522 (tt0) cc_final: 0.7221 (tt0) REVERT: B 220 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8031 (pt0) REVERT: B 227 GLU cc_start: 0.8090 (tt0) cc_final: 0.7880 (tt0) REVERT: B 253 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8086 (t) REVERT: B 278 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8168 (mtpt) REVERT: C 47 MET cc_start: 0.6656 (mmp) cc_final: 0.6048 (tmt) REVERT: C 155 MET cc_start: 0.8762 (ptt) cc_final: 0.8462 (ptt) REVERT: C 181 GLU cc_start: 0.8039 (tp30) cc_final: 0.7442 (mp0) REVERT: C 273 MET cc_start: 0.8027 (ttm) cc_final: 0.7741 (ttp) REVERT: D 47 MET cc_start: 0.6756 (mmp) cc_final: 0.6178 (tmm) REVERT: D 60 LYS cc_start: 0.7308 (ptmm) cc_final: 0.7027 (ptpp) REVERT: D 149 GLN cc_start: 0.8251 (mt0) cc_final: 0.7927 (mm110) REVERT: D 181 GLU cc_start: 0.8081 (tp30) cc_final: 0.7504 (mp0) REVERT: D 210 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: E 47 MET cc_start: 0.6479 (mmp) cc_final: 0.6134 (tmt) REVERT: E 181 GLU cc_start: 0.8147 (tp30) cc_final: 0.7628 (tt0) REVERT: E 227 GLU cc_start: 0.8048 (tt0) cc_final: 0.7719 (tt0) REVERT: F 47 MET cc_start: 0.6984 (mmp) cc_final: 0.6429 (tmm) REVERT: F 92 GLN cc_start: 0.8281 (tt0) cc_final: 0.7947 (tt0) REVERT: F 134 GLU cc_start: 0.8146 (tt0) cc_final: 0.7883 (tt0) REVERT: F 155 MET cc_start: 0.8448 (ptt) cc_final: 0.8115 (ptm) REVERT: F 210 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: F 227 GLU cc_start: 0.8077 (tt0) cc_final: 0.7749 (tt0) REVERT: G 47 MET cc_start: 0.6779 (mmp) cc_final: 0.6286 (tmm) REVERT: G 60 LYS cc_start: 0.7448 (ptmm) cc_final: 0.7207 (ptpp) REVERT: G 72 LEU cc_start: 0.7520 (tp) cc_final: 0.7298 (tt) REVERT: G 134 GLU cc_start: 0.8213 (tt0) cc_final: 0.7956 (tt0) REVERT: G 135 TYR cc_start: 0.8553 (t80) cc_final: 0.8344 (t80) REVERT: G 181 GLU cc_start: 0.7988 (tp30) cc_final: 0.7435 (mp0) REVERT: G 247 GLN cc_start: 0.8311 (tp40) cc_final: 0.8062 (tp-100) REVERT: G 278 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8225 (mtmt) outliers start: 48 outliers final: 16 residues processed: 241 average time/residue: 1.3318 time to fit residues: 352.2308 Evaluate side-chains 223 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 237 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 0.0770 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 149 GLN A 203 GLN B 92 GLN B 149 GLN B 203 GLN C 92 GLN C 149 GLN E 92 GLN E 149 GLN F 149 GLN G 149 GLN G 210 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15477 Z= 0.252 Angle : 0.488 9.039 20776 Z= 0.253 Chirality : 0.041 0.146 2415 Planarity : 0.004 0.057 2548 Dihedral : 17.259 164.126 2961 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.92 % Allowed : 20.93 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.19), residues: 1841 helix: 2.27 (0.16), residues: 987 sheet: -0.09 (0.28), residues: 308 loop : -1.00 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 240 PHE 0.018 0.002 PHE D 127 TYR 0.013 0.001 TYR E 27 ARG 0.006 0.000 ARG D 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 201 time to evaluate : 1.664 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6463 (mmp) cc_final: 0.5938 (tmt) REVERT: A 153 THR cc_start: 0.9468 (p) cc_final: 0.9239 (t) REVERT: A 278 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8098 (mtpt) REVERT: B 47 MET cc_start: 0.6879 (mmp) cc_final: 0.6407 (tmm) REVERT: B 68 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.6281 (p90) REVERT: B 149 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7913 (mm110) REVERT: B 159 ASP cc_start: 0.7929 (t70) cc_final: 0.7681 (t0) REVERT: B 171 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8696 (mp) REVERT: B 181 GLU cc_start: 0.7531 (tt0) cc_final: 0.7290 (tt0) REVERT: B 187 GLU cc_start: 0.8145 (tt0) cc_final: 0.7846 (tt0) REVERT: B 220 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8091 (pt0) REVERT: B 227 GLU cc_start: 0.8081 (tt0) cc_final: 0.7857 (tt0) REVERT: B 253 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8176 (t) REVERT: B 278 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8182 (mtpt) REVERT: C 47 MET cc_start: 0.6688 (mmp) cc_final: 0.6051 (tmt) REVERT: C 155 MET cc_start: 0.8790 (ptt) cc_final: 0.8466 (ptt) REVERT: C 181 GLU cc_start: 0.8091 (tp30) cc_final: 0.7405 (mp0) REVERT: C 273 MET cc_start: 0.8029 (ttm) cc_final: 0.7741 (ttp) REVERT: D 47 MET cc_start: 0.6719 (mmp) cc_final: 0.6015 (tmm) REVERT: D 60 LYS cc_start: 0.7330 (ptmm) cc_final: 0.7057 (ptpp) REVERT: D 149 GLN cc_start: 0.8242 (mt0) cc_final: 0.7938 (mm110) REVERT: D 210 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: E 47 MET cc_start: 0.6583 (mmp) cc_final: 0.6190 (tmt) REVERT: E 227 GLU cc_start: 0.8092 (tt0) cc_final: 0.7771 (tt0) REVERT: F 47 MET cc_start: 0.6999 (mmp) cc_final: 0.6425 (tmm) REVERT: F 92 GLN cc_start: 0.8396 (tt0) cc_final: 0.8137 (tt0) REVERT: F 134 GLU cc_start: 0.8240 (tt0) cc_final: 0.7978 (tt0) REVERT: F 155 MET cc_start: 0.8440 (ptt) cc_final: 0.8101 (ptm) REVERT: F 210 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: F 227 GLU cc_start: 0.8102 (tt0) cc_final: 0.7767 (tt0) REVERT: F 273 MET cc_start: 0.7926 (ttm) cc_final: 0.7509 (ttp) REVERT: G 47 MET cc_start: 0.6784 (mmp) cc_final: 0.6296 (tmm) REVERT: G 60 LYS cc_start: 0.7424 (ptmm) cc_final: 0.7175 (ptpp) REVERT: G 72 LEU cc_start: 0.7518 (tp) cc_final: 0.7300 (tt) REVERT: G 134 GLU cc_start: 0.8202 (tt0) cc_final: 0.7907 (tt0) REVERT: G 149 GLN cc_start: 0.8258 (mt0) cc_final: 0.7878 (mm110) REVERT: G 247 GLN cc_start: 0.8348 (tp40) cc_final: 0.8113 (tp-100) REVERT: G 278 LYS cc_start: 0.8494 (mtpt) cc_final: 0.7927 (mtmt) outliers start: 44 outliers final: 19 residues processed: 233 average time/residue: 1.3864 time to fit residues: 353.3421 Evaluate side-chains 224 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 149 GLN A 203 GLN B 92 GLN B 203 GLN C 92 GLN C 149 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN E 149 GLN F 149 GLN G 207 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15477 Z= 0.165 Angle : 0.471 10.026 20776 Z= 0.240 Chirality : 0.040 0.133 2415 Planarity : 0.004 0.056 2548 Dihedral : 16.992 164.814 2961 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.66 % Allowed : 21.00 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.19), residues: 1841 helix: 2.41 (0.16), residues: 987 sheet: -0.03 (0.28), residues: 308 loop : -0.96 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 16 PHE 0.017 0.002 PHE E 68 TYR 0.013 0.001 TYR E 27 ARG 0.007 0.000 ARG D 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 1.787 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6603 (mmp) cc_final: 0.5936 (tmt) REVERT: A 149 GLN cc_start: 0.8063 (mt0) cc_final: 0.7731 (mm110) REVERT: A 181 GLU cc_start: 0.8039 (tp30) cc_final: 0.7822 (mm-30) REVERT: A 278 LYS cc_start: 0.8572 (mtpt) cc_final: 0.8142 (mtpt) REVERT: B 47 MET cc_start: 0.6872 (mmp) cc_final: 0.6415 (tmm) REVERT: B 68 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.6305 (p90) REVERT: B 159 ASP cc_start: 0.7873 (t70) cc_final: 0.7635 (t0) REVERT: B 171 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8658 (mp) REVERT: B 181 GLU cc_start: 0.7489 (tt0) cc_final: 0.7192 (tt0) REVERT: B 187 GLU cc_start: 0.8132 (tt0) cc_final: 0.7839 (tt0) REVERT: B 220 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8033 (pt0) REVERT: B 227 GLU cc_start: 0.8083 (tt0) cc_final: 0.7861 (tt0) REVERT: B 253 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8136 (t) REVERT: B 278 LYS cc_start: 0.8499 (mtmm) cc_final: 0.8213 (mtpt) REVERT: C 47 MET cc_start: 0.6686 (mmp) cc_final: 0.6061 (tmt) REVERT: C 155 MET cc_start: 0.8756 (ptt) cc_final: 0.8439 (ptt) REVERT: C 181 GLU cc_start: 0.8074 (tp30) cc_final: 0.7402 (mp0) REVERT: C 203 GLN cc_start: 0.7839 (tp40) cc_final: 0.7404 (tp-100) REVERT: C 273 MET cc_start: 0.8030 (ttm) cc_final: 0.7746 (ttp) REVERT: D 47 MET cc_start: 0.6639 (mmp) cc_final: 0.6018 (tmm) REVERT: D 149 GLN cc_start: 0.8229 (mt0) cc_final: 0.7922 (mm110) REVERT: D 181 GLU cc_start: 0.7970 (tp30) cc_final: 0.7548 (mp0) REVERT: D 210 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: D 227 GLU cc_start: 0.8096 (tt0) cc_final: 0.7832 (tt0) REVERT: E 47 MET cc_start: 0.6581 (mmp) cc_final: 0.6197 (tmt) REVERT: E 181 GLU cc_start: 0.8069 (tp30) cc_final: 0.7703 (tt0) REVERT: E 227 GLU cc_start: 0.8073 (tt0) cc_final: 0.7738 (tt0) REVERT: F 47 MET cc_start: 0.7005 (mmp) cc_final: 0.6446 (tmm) REVERT: F 92 GLN cc_start: 0.8337 (tt0) cc_final: 0.8070 (tt0) REVERT: F 105 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8003 (tt) REVERT: F 134 GLU cc_start: 0.8211 (tt0) cc_final: 0.7965 (tt0) REVERT: F 153 THR cc_start: 0.9344 (p) cc_final: 0.9090 (t) REVERT: F 155 MET cc_start: 0.8457 (ptt) cc_final: 0.8038 (ptm) REVERT: F 210 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: F 227 GLU cc_start: 0.8075 (tt0) cc_final: 0.7746 (tt0) REVERT: G 47 MET cc_start: 0.6783 (mmp) cc_final: 0.6305 (tmm) REVERT: G 60 LYS cc_start: 0.7406 (ptmm) cc_final: 0.7167 (ptpp) REVERT: G 134 GLU cc_start: 0.8195 (tt0) cc_final: 0.7918 (tt0) REVERT: G 149 GLN cc_start: 0.8259 (mt0) cc_final: 0.7882 (mm110) REVERT: G 203 GLN cc_start: 0.7743 (tp40) cc_final: 0.7467 (tp40) REVERT: G 247 GLN cc_start: 0.8305 (tp40) cc_final: 0.8049 (tp-100) REVERT: G 278 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8180 (mtmt) outliers start: 40 outliers final: 18 residues processed: 238 average time/residue: 1.3911 time to fit residues: 362.0711 Evaluate side-chains 228 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 181 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN B 92 GLN B 203 GLN C 92 GLN C 149 GLN E 92 GLN E 149 GLN G 203 GLN G 207 ASN G 210 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15477 Z= 0.167 Angle : 0.475 9.930 20776 Z= 0.241 Chirality : 0.040 0.134 2415 Planarity : 0.003 0.055 2548 Dihedral : 16.692 166.450 2961 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.26 % Allowed : 21.33 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 1841 helix: 2.46 (0.16), residues: 987 sheet: 0.01 (0.28), residues: 308 loop : -0.94 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 16 PHE 0.017 0.002 PHE E 68 TYR 0.024 0.001 TYR F 27 ARG 0.008 0.000 ARG D 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 214 time to evaluate : 1.692 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6479 (mmp) cc_final: 0.5944 (tmt) REVERT: A 149 GLN cc_start: 0.8032 (mt0) cc_final: 0.7706 (mm110) REVERT: A 278 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8162 (mtpt) REVERT: B 47 MET cc_start: 0.6868 (mmp) cc_final: 0.6356 (tmt) REVERT: B 68 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6351 (p90) REVERT: B 159 ASP cc_start: 0.7880 (t70) cc_final: 0.7642 (t0) REVERT: B 171 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8668 (mp) REVERT: B 181 GLU cc_start: 0.7485 (tt0) cc_final: 0.7216 (tt0) REVERT: B 187 GLU cc_start: 0.8145 (tt0) cc_final: 0.7850 (tt0) REVERT: B 220 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: B 227 GLU cc_start: 0.8092 (tt0) cc_final: 0.7881 (tt0) REVERT: B 253 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8087 (t) REVERT: B 278 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8256 (mtpp) REVERT: C 47 MET cc_start: 0.6637 (mmp) cc_final: 0.6200 (tmm) REVERT: C 155 MET cc_start: 0.8767 (ptt) cc_final: 0.8475 (ptt) REVERT: C 181 GLU cc_start: 0.8075 (tp30) cc_final: 0.7402 (mp0) REVERT: C 273 MET cc_start: 0.8043 (ttm) cc_final: 0.7755 (ttp) REVERT: D 47 MET cc_start: 0.6803 (mmp) cc_final: 0.6195 (tmm) REVERT: D 149 GLN cc_start: 0.8256 (mt0) cc_final: 0.7941 (mm110) REVERT: D 181 GLU cc_start: 0.8015 (tp30) cc_final: 0.7574 (mp0) REVERT: D 210 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: D 227 GLU cc_start: 0.8094 (tt0) cc_final: 0.7831 (tt0) REVERT: E 47 MET cc_start: 0.6606 (mmp) cc_final: 0.6225 (tmt) REVERT: E 181 GLU cc_start: 0.8088 (tp30) cc_final: 0.7703 (tt0) REVERT: E 227 GLU cc_start: 0.8070 (tt0) cc_final: 0.7739 (tt0) REVERT: F 47 MET cc_start: 0.7013 (mmp) cc_final: 0.6445 (tmm) REVERT: F 92 GLN cc_start: 0.8333 (tt0) cc_final: 0.8000 (tt0) REVERT: F 105 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8006 (tt) REVERT: F 134 GLU cc_start: 0.8197 (tt0) cc_final: 0.7945 (tt0) REVERT: F 155 MET cc_start: 0.8450 (ptt) cc_final: 0.8096 (ptm) REVERT: F 210 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: F 212 GLU cc_start: 0.7898 (tp30) cc_final: 0.7594 (mm-30) REVERT: F 227 GLU cc_start: 0.8079 (tt0) cc_final: 0.7763 (tt0) REVERT: G 47 MET cc_start: 0.6778 (mmp) cc_final: 0.6301 (tmm) REVERT: G 60 LYS cc_start: 0.7365 (ptmm) cc_final: 0.7137 (ptpp) REVERT: G 134 GLU cc_start: 0.8196 (tt0) cc_final: 0.7916 (tt0) REVERT: G 149 GLN cc_start: 0.8281 (mt0) cc_final: 0.7887 (mm110) REVERT: G 278 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8156 (mtmt) outliers start: 34 outliers final: 19 residues processed: 238 average time/residue: 1.3698 time to fit residues: 356.6795 Evaluate side-chains 227 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 201 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 40 optimal weight: 0.0770 chunk 144 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN B 92 GLN B 207 ASN C 92 GLN E 92 GLN F 203 GLN G 210 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.092002 restraints weight = 21129.387| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.18 r_work: 0.3021 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15477 Z= 0.149 Angle : 0.477 9.832 20776 Z= 0.241 Chirality : 0.040 0.129 2415 Planarity : 0.003 0.055 2548 Dihedral : 16.339 167.634 2961 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.99 % Allowed : 22.06 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.20), residues: 1841 helix: 2.56 (0.16), residues: 987 sheet: 0.07 (0.28), residues: 308 loop : -0.94 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 16 PHE 0.016 0.001 PHE E 68 TYR 0.019 0.001 TYR F 27 ARG 0.007 0.000 ARG D 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6167.98 seconds wall clock time: 109 minutes 48.18 seconds (6588.18 seconds total)