Starting phenix.real_space_refine on Fri Sep 11 07:52:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24vi_69840/09_2026/24vi_69840_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/24vi_69840/09_2026/24vi_69840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/24vi_69840/09_2026/24vi_69840_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24vi_69840/09_2026/24vi_69840_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/24vi_69840/09_2026/24vi_69840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24vi_69840/09_2026/24vi_69840.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.147 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 3 5.49 5 S 37 5.16 5 C 5508 2.51 5 N 1319 2.21 5 O 1397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8264 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1913 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1982 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 4, 'TRANS': 238} Chain breaks: 1 Chain: "C" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 2000 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 4, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2006 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 4, 'TRANS': 242} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'9PE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 121 Unusual residues: {'9PE': 1, 'YJ0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 81 Unusual residues: {'YJ0': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 121 Unusual residues: {'9PE': 1, 'YJ0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.00, per 1000 atoms: 0.24 Number of scatterers: 8264 At special positions: 0 Unit cell: (84.0294, 105.575, 113.117, 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 37 16.00 P 3 15.00 O 1397 8.00 N 1319 7.00 C 5508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 424.6 milliseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 124 through 143 Processing helix chain 'A' and resid 149 through 178 removed outlier: 4.015A pdb=" N TRP A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 229 through 238 removed outlier: 3.938A pdb=" N GLN A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 removed outlier: 4.246A pdb=" N LEU A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 283 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 327 through 345 removed outlier: 3.672A pdb=" N LEU A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.633A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 91 through 113 removed outlier: 3.864A pdb=" N HIS B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 147 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.858A pdb=" N ILE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.631A pdb=" N ALA B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 253 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 305 removed outlier: 3.723A pdb=" N ALA B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 326 removed outlier: 3.557A pdb=" N LYS B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 91 through 112 removed outlier: 4.227A pdb=" N HIS C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 147 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 155 through 164 Processing helix chain 'C' and resid 165 through 183 Processing helix chain 'C' and resid 201 through 209 removed outlier: 4.163A pdb=" N LEU C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 228 through 253 removed outlier: 3.518A pdb=" N VAL C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 286 through 326 removed outlier: 3.878A pdb=" N LEU C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Proline residue: C 307 - end of helix removed outlier: 3.623A pdb=" N LEU C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 93 through 114 removed outlier: 3.686A pdb=" N ILE D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 145 removed outlier: 3.677A pdb=" N SER D 121 " --> pdb=" O TYR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 165 through 183 Processing helix chain 'D' and resid 201 through 209 removed outlier: 3.754A pdb=" N LEU D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 230 through 253 removed outlier: 3.654A pdb=" N ALA D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.648A pdb=" N ALA D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 326 removed outlier: 3.662A pdb=" N GLY D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1701 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: 1.26 Time building geometry restraints manager: 0.95 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: 1162 1.31 - 1.43: 2562 1.43 - 1.56: 4716 1.56 - 1.69: 7 1.69 - 1.81: 50 Bond restraints: 8497 Sorted by residual: bond pdb=" C31 9PE D1001 " pdb=" O31 9PE D1001 " ideal model delta sigma weight residual 1.325 1.399 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C31 9PE A1001 " pdb=" O31 9PE A1001 " ideal model delta sigma weight residual 1.325 1.399 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C31 9PE B 602 " pdb=" O31 9PE B 602 " ideal model delta sigma weight residual 1.325 1.399 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C21 9PE B 602 " pdb=" O21 9PE B 602 " ideal model delta sigma weight residual 1.329 1.401 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C21 9PE D1001 " pdb=" O21 9PE D1001 " ideal model delta sigma weight residual 1.329 1.399 -0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 8492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 11208 2.43 - 4.85: 193 4.85 - 7.28: 90 7.28 - 9.70: 29 9.70 - 12.13: 8 Bond angle restraints: 11528 Sorted by residual: angle pdb=" O12 9PE B 602 " pdb=" P 9PE B 602 " pdb=" O14 9PE B 602 " ideal model delta sigma weight residual 120.90 108.77 12.13 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O12 9PE A1001 " pdb=" P 9PE A1001 " pdb=" O14 9PE A1001 " ideal model delta sigma weight residual 120.90 109.25 11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O12 9PE D1001 " pdb=" P 9PE D1001 " pdb=" O14 9PE D1001 " ideal model delta sigma weight residual 120.90 109.36 11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C12 YJ0 B 601 " pdb=" C7 YJ0 B 601 " pdb=" C6 YJ0 B 601 " ideal model delta sigma weight residual 118.64 129.85 -11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" C PRO B 87 " pdb=" N ARG B 88 " pdb=" CA ARG B 88 " ideal model delta sigma weight residual 121.54 128.64 -7.10 1.91e+00 2.74e-01 1.38e+01 ... (remaining 11523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 4786 35.46 - 70.93: 332 70.93 - 106.39: 111 106.39 - 141.85: 82 141.85 - 177.32: 30 Dihedral angle restraints: 5341 sinusoidal: 2528 harmonic: 2813 Sorted by residual: dihedral pdb=" O36 YJ0 D1002 " pdb=" C31 YJ0 D1002 " pdb=" C32 YJ0 D1002 " pdb=" O52 YJ0 D1002 " ideal model delta sinusoidal sigma weight residual 124.08 -58.60 -177.32 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O30 YJ0 D1002 " pdb=" C31 YJ0 D1002 " pdb=" C32 YJ0 D1002 " pdb=" O52 YJ0 D1002 " ideal model delta sinusoidal sigma weight residual 234.92 61.19 173.73 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O63 YJ0 B 601 " pdb=" C64 YJ0 B 601 " pdb=" C65 YJ0 B 601 " pdb=" O74 YJ0 B 601 " ideal model delta sinusoidal sigma weight residual 49.21 -123.83 173.04 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.214: 1284 1.214 - 2.429: 0 2.429 - 3.643: 0 3.643 - 4.858: 5 4.858 - 6.072: 29 Chirality restraints: 1318 Sorted by residual: chirality pdb=" C12 YJ0 D1002 " pdb=" C11 YJ0 D1002 " pdb=" C13 YJ0 D1002 " pdb=" C7 YJ0 D1002 " both_signs ideal model delta sigma weight residual False 3.10 -2.98 6.07 2.00e-01 2.50e+01 9.22e+02 chirality pdb=" C12 YJ0 C 601 " pdb=" C11 YJ0 C 601 " pdb=" C13 YJ0 C 601 " pdb=" C7 YJ0 C 601 " both_signs ideal model delta sigma weight residual False 3.10 -2.95 6.05 2.00e-01 2.50e+01 9.15e+02 chirality pdb=" C8 YJ0 B 601 " pdb=" C10 YJ0 B 601 " pdb=" C7 YJ0 B 601 " pdb=" O9 YJ0 B 601 " both_signs ideal model delta sigma weight residual False -2.87 2.73 -5.60 2.00e-01 2.50e+01 7.83e+02 ... (remaining 1315 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 C 601 " -0.156 2.00e-02 2.50e+03 1.31e-01 2.16e+02 pdb=" C18 YJ0 C 601 " 0.189 2.00e-02 2.50e+03 pdb=" C19 YJ0 C 601 " 0.092 2.00e-02 2.50e+03 pdb=" C20 YJ0 C 601 " 0.008 2.00e-02 2.50e+03 pdb=" C24 YJ0 C 601 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 D1002 " 0.108 2.00e-02 2.50e+03 8.98e-02 1.01e+02 pdb=" C18 YJ0 D1002 " -0.133 2.00e-02 2.50e+03 pdb=" C19 YJ0 D1002 " -0.052 2.00e-02 2.50e+03 pdb=" C20 YJ0 D1002 " -0.012 2.00e-02 2.50e+03 pdb=" C24 YJ0 D1002 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 293 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" C ALA B 293 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA B 293 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA B 294 " 0.014 2.00e-02 2.50e+03 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1348 2.76 - 3.29: 7958 3.29 - 3.83: 13847 3.83 - 4.36: 15188 4.36 - 4.90: 26923 Nonbonded interactions: 65264 Sorted by model distance: nonbonded pdb=" O ARG C 88 " pdb=" NH1 ARG C 88 " model vdw 2.220 3.120 nonbonded pdb=" NH1 ARG D 212 " pdb=" O38 YJ0 D1002 " model vdw 2.221 3.120 nonbonded pdb=" OH TYR A 319 " pdb=" OG1 THR D 273 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR B 94 " pdb=" OE1 GLU B 139 " model vdw 2.260 3.040 nonbonded pdb=" O VAL D 110 " pdb=" OG1 THR D 113 " model vdw 2.264 3.040 ... (remaining 65259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 70 through 326) selection = (chain 'C' and (resid 70 through 182 or resid 197 through 326)) selection = (chain 'D' and (resid 70 through 182 or resid 197 through 326)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.160 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.005 0.074 8497 Z= 0.254 Angle : 0.984 12.128 11528 Z= 0.418 Chirality : 0.836 6.072 1318 Planarity : 0.006 0.131 1334 Dihedral : 34.375 177.318 3545 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.47 % Favored : 93.01 % Rotamer: Outliers : 1.60 % Allowed : 32.43 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.28), residues: 959 helix: 1.44 (0.19), residues: 751 sheet: None (None), residues: 0 loop : -3.25 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 212 TYR 0.010 0.001 TYR D 73 PHE 0.013 0.001 PHE D 136 TRP 0.015 0.001 TRP D 287 HIS 0.003 0.001 HIS D 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.25 ( 8497) covalent geometry : angle 0.98411 / 0.42 (11528) hydrogen bonds : bond 0.12775 / 8.65 ( 571) hydrogen bonds : angle 5.49292 / 3.98 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7804 (mmt180) cc_final: 0.5540 (ptp90) REVERT: A 296 MET cc_start: 0.4789 (tpt) cc_final: 0.3506 (ptp) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 0.5839 time to fit residues: 56.5340 Evaluate side-chains 87 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 243 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.219287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.151318 restraints weight = 8533.334| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.24 r_work: 0.3481 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8497 Z= 0.154 Angle : 1.251 36.562 11528 Z= 0.473 Chirality : 0.130 2.324 1318 Planarity : 0.004 0.054 1334 Dihedral : 28.570 178.892 1806 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.05 % Favored : 93.53 % Rotamer: Outliers : 4.56 % Allowed : 29.35 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.28), residues: 959 helix: 1.60 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -3.08 (0.37), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 212 TYR 0.012 0.001 TYR B 81 PHE 0.013 0.001 PHE D 136 TRP 0.017 0.001 TRP D 156 HIS 0.009 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 ( 8497) covalent geometry : angle 1.25078 / 0.47 (11528) hydrogen bonds : bond 0.05342 / 3.58 ( 571) hydrogen bonds : angle 4.36004 / 3.14 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.297 Fit side-chains REVERT: A 242 ARG cc_start: 0.6692 (tpp-160) cc_final: 0.5381 (pmm150) REVERT: B 73 TYR cc_start: 0.4538 (OUTLIER) cc_final: 0.3975 (m-80) REVERT: B 212 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6336 (mtt90) REVERT: B 286 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7722 (p) REVERT: C 151 CYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6124 (t) REVERT: D 116 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6866 (pt0) REVERT: D 164 ARG cc_start: 0.5634 (ptm-80) cc_final: 0.4706 (tpt90) outliers start: 37 outliers final: 11 residues processed: 111 average time/residue: 0.5557 time to fit residues: 65.7958 Evaluate side-chains 97 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 0.0270 chunk 1 optimal weight: 20.0000 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.219312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.151197 restraints weight = 8400.557| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.21 r_work: 0.3485 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8497 Z= 0.143 Angle : 1.176 34.464 11528 Z= 0.446 Chirality : 0.128 2.184 1318 Planarity : 0.004 0.054 1334 Dihedral : 26.578 177.698 1796 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.05 % Favored : 93.64 % Rotamer: Outliers : 5.06 % Allowed : 28.73 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.28), residues: 959 helix: 1.72 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -2.86 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 154 TYR 0.011 0.001 TYR B 81 PHE 0.011 0.001 PHE D 136 TRP 0.014 0.001 TRP D 287 HIS 0.002 0.000 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 8497) covalent geometry : angle 1.17589 / 0.45 (11528) hydrogen bonds : bond 0.05253 / 3.52 ( 571) hydrogen bonds : angle 4.17614 / 3.00 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.3005 (OUTLIER) cc_final: 0.1843 (m-10) REVERT: B 73 TYR cc_start: 0.4553 (OUTLIER) cc_final: 0.3870 (t80) REVERT: B 78 ASN cc_start: 0.7836 (t0) cc_final: 0.7557 (t0) REVERT: B 286 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7670 (p) REVERT: C 151 CYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6131 (t) REVERT: C 233 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7756 (m) REVERT: D 164 ARG cc_start: 0.5735 (ptm-80) cc_final: 0.4681 (tpt90) outliers start: 41 outliers final: 17 residues processed: 116 average time/residue: 0.5775 time to fit residues: 71.0689 Evaluate side-chains 102 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 320 GLN D 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.215447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145492 restraints weight = 8561.037| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.25 r_work: 0.3405 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8497 Z= 0.185 Angle : 1.195 35.341 11528 Z= 0.460 Chirality : 0.125 2.106 1318 Planarity : 0.004 0.056 1334 Dihedral : 25.530 177.426 1796 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.57 % Favored : 93.22 % Rotamer: Outliers : 5.30 % Allowed : 28.36 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.28), residues: 959 helix: 1.59 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -2.86 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 154 TYR 0.011 0.001 TYR C 236 PHE 0.014 0.002 PHE D 239 TRP 0.012 0.001 TRP D 287 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 8497) covalent geometry : angle 1.19529 / 0.46 (11528) hydrogen bonds : bond 0.05877 / 3.92 ( 571) hydrogen bonds : angle 4.23673 / 3.04 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 81 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.3014 (OUTLIER) cc_final: 0.1811 (m-10) REVERT: A 296 MET cc_start: 0.5541 (tpt) cc_final: 0.4144 (ptp) REVERT: B 73 TYR cc_start: 0.4634 (OUTLIER) cc_final: 0.4047 (m-80) REVERT: B 88 ARG cc_start: 0.4670 (OUTLIER) cc_final: 0.3221 (ptm-80) REVERT: B 276 THR cc_start: 0.8288 (p) cc_final: 0.7912 (p) REVERT: B 286 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8060 (p) REVERT: C 151 CYS cc_start: 0.6780 (OUTLIER) cc_final: 0.5996 (t) REVERT: D 167 PHE cc_start: 0.4275 (OUTLIER) cc_final: 0.3537 (t80) outliers start: 43 outliers final: 23 residues processed: 115 average time/residue: 0.6165 time to fit residues: 75.1781 Evaluate side-chains 107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 GLN C 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.216728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148622 restraints weight = 8514.931| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.32 r_work: 0.3446 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8497 Z= 0.152 Angle : 1.167 34.833 11528 Z= 0.445 Chirality : 0.124 2.107 1318 Planarity : 0.004 0.055 1334 Dihedral : 25.012 176.627 1794 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 5.43 % Allowed : 29.10 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.28), residues: 959 helix: 1.73 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -2.84 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 164 TYR 0.010 0.001 TYR C 236 PHE 0.012 0.001 PHE D 167 TRP 0.011 0.001 TRP D 145 HIS 0.002 0.000 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 8497) covalent geometry : angle 1.16716 / 0.45 (11528) hydrogen bonds : bond 0.05402 / 3.61 ( 571) hydrogen bonds : angle 4.15488 / 2.97 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.3058 (OUTLIER) cc_final: 0.1888 (m-10) REVERT: A 242 ARG cc_start: 0.6861 (tpp-160) cc_final: 0.5634 (pmt170) REVERT: A 243 ARG cc_start: 0.7530 (mmt180) cc_final: 0.7278 (mmt180) REVERT: A 296 MET cc_start: 0.5493 (tpt) cc_final: 0.4302 (ptp) REVERT: B 73 TYR cc_start: 0.4539 (OUTLIER) cc_final: 0.3960 (m-80) REVERT: B 88 ARG cc_start: 0.4292 (OUTLIER) cc_final: 0.2905 (ptm-80) REVERT: B 276 THR cc_start: 0.8334 (p) cc_final: 0.7832 (p) REVERT: B 286 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7738 (p) REVERT: C 151 CYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6101 (t) REVERT: C 233 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7815 (m) REVERT: D 167 PHE cc_start: 0.4075 (OUTLIER) cc_final: 0.3031 (t80) outliers start: 44 outliers final: 23 residues processed: 112 average time/residue: 0.5888 time to fit residues: 70.1115 Evaluate side-chains 106 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 62 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 3 optimal weight: 0.0000 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 320 GLN D 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.213426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142366 restraints weight = 8438.296| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.68 r_work: 0.3370 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8497 Z= 0.186 Angle : 1.180 34.928 11528 Z= 0.455 Chirality : 0.124 2.101 1318 Planarity : 0.004 0.056 1334 Dihedral : 24.760 176.848 1792 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.47 % Favored : 93.33 % Rotamer: Outliers : 6.29 % Allowed : 28.36 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.28), residues: 959 helix: 1.63 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -2.91 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 157 TYR 0.011 0.001 TYR C 236 PHE 0.014 0.001 PHE D 239 TRP 0.016 0.001 TRP D 287 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 8497) covalent geometry : angle 1.18019 / 0.45 (11528) hydrogen bonds : bond 0.05784 / 3.85 ( 571) hydrogen bonds : angle 4.20836 / 3.01 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 78 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.3217 (OUTLIER) cc_final: 0.2045 (m-10) REVERT: A 242 ARG cc_start: 0.6764 (tpp-160) cc_final: 0.5611 (pmt170) REVERT: A 296 MET cc_start: 0.5632 (tpt) cc_final: 0.4247 (ptp) REVERT: B 73 TYR cc_start: 0.4497 (OUTLIER) cc_final: 0.3924 (m-80) REVERT: B 88 ARG cc_start: 0.4254 (OUTLIER) cc_final: 0.2883 (ptm-80) REVERT: B 141 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6464 (m-10) REVERT: B 210 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6729 (mtm) REVERT: B 253 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: B 276 THR cc_start: 0.8374 (p) cc_final: 0.7996 (p) REVERT: B 286 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7840 (p) REVERT: C 106 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5914 (mp) REVERT: C 151 CYS cc_start: 0.6679 (OUTLIER) cc_final: 0.5860 (t) REVERT: C 233 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7877 (m) REVERT: D 167 PHE cc_start: 0.4109 (OUTLIER) cc_final: 0.3173 (t80) outliers start: 51 outliers final: 30 residues processed: 117 average time/residue: 0.5742 time to fit residues: 71.0825 Evaluate side-chains 114 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 73 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 7 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 0.0770 chunk 80 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.214978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147852 restraints weight = 8501.114| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.38 r_work: 0.3421 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8497 Z= 0.137 Angle : 1.155 34.579 11528 Z= 0.439 Chirality : 0.124 2.097 1318 Planarity : 0.004 0.054 1334 Dihedral : 24.477 177.193 1792 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.94 % Favored : 93.85 % Rotamer: Outliers : 5.43 % Allowed : 29.59 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.28), residues: 959 helix: 1.81 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -2.89 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 154 TYR 0.010 0.001 TYR C 236 PHE 0.011 0.001 PHE D 239 TRP 0.010 0.001 TRP D 145 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 ( 8497) covalent geometry : angle 1.15508 / 0.44 (11528) hydrogen bonds : bond 0.05223 / 3.49 ( 571) hydrogen bonds : angle 4.10366 / 2.93 ( 1701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 76 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.3245 (OUTLIER) cc_final: 0.2092 (m-10) REVERT: A 242 ARG cc_start: 0.6727 (tpp-160) cc_final: 0.5647 (pmt170) REVERT: A 243 ARG cc_start: 0.7456 (mmt180) cc_final: 0.7243 (mmt180) REVERT: A 296 MET cc_start: 0.5586 (tpt) cc_final: 0.4234 (ptp) REVERT: B 73 TYR cc_start: 0.4475 (OUTLIER) cc_final: 0.3913 (m-80) REVERT: B 141 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6365 (m-10) REVERT: B 276 THR cc_start: 0.8318 (p) cc_final: 0.7838 (p) REVERT: B 286 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7698 (p) REVERT: C 106 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5884 (mp) REVERT: C 151 CYS cc_start: 0.6756 (OUTLIER) cc_final: 0.5980 (t) REVERT: C 233 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7785 (m) REVERT: D 167 PHE cc_start: 0.4054 (OUTLIER) cc_final: 0.3136 (t80) outliers start: 44 outliers final: 25 residues processed: 111 average time/residue: 0.5719 time to fit residues: 67.2708 Evaluate side-chains 107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 324 ARG Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 31 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 73 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.214961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147715 restraints weight = 8457.215| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.31 r_work: 0.3425 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8497 Z= 0.140 Angle : 1.154 34.481 11528 Z= 0.439 Chirality : 0.123 2.089 1318 Planarity : 0.004 0.054 1334 Dihedral : 24.284 177.637 1792 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.05 % Favored : 93.85 % Rotamer: Outliers : 5.67 % Allowed : 29.47 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.28), residues: 959 helix: 1.82 (0.19), residues: 765 sheet: None (None), residues: 0 loop : -2.85 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 157 TYR 0.009 0.001 TYR D 73 PHE 0.011 0.001 PHE D 239 TRP 0.018 0.001 TRP D 287 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 8497) covalent geometry : angle 1.15437 / 0.44 (11528) hydrogen bonds : bond 0.05224 / 3.49 ( 571) hydrogen bonds : angle 4.07919 / 2.91 ( 1701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 81 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.3245 (OUTLIER) cc_final: 0.2142 (m-10) REVERT: A 242 ARG cc_start: 0.6859 (tpp-160) cc_final: 0.5659 (pmt170) REVERT: A 284 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6703 (mtpp) REVERT: A 296 MET cc_start: 0.5663 (tpt) cc_final: 0.4387 (ptp) REVERT: B 73 TYR cc_start: 0.4555 (OUTLIER) cc_final: 0.3923 (m-80) REVERT: B 210 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6802 (mtm) REVERT: B 253 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: B 276 THR cc_start: 0.8310 (p) cc_final: 0.7799 (p) REVERT: B 286 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7723 (p) REVERT: C 106 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5911 (mp) REVERT: C 151 CYS cc_start: 0.6732 (OUTLIER) cc_final: 0.5957 (t) REVERT: C 233 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7801 (m) REVERT: D 167 PHE cc_start: 0.4151 (OUTLIER) cc_final: 0.3234 (t80) outliers start: 46 outliers final: 26 residues processed: 119 average time/residue: 0.5747 time to fit residues: 72.7683 Evaluate side-chains 113 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 77 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 324 ARG Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 0.0270 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 GLN D 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.215192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147612 restraints weight = 8454.414| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.42 r_work: 0.3424 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8497 Z= 0.139 Angle : 1.151 34.392 11528 Z= 0.437 Chirality : 0.123 2.084 1318 Planarity : 0.004 0.054 1334 Dihedral : 24.150 178.053 1792 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.74 % Rotamer: Outliers : 4.93 % Allowed : 29.84 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.28), residues: 959 helix: 1.87 (0.19), residues: 765 sheet: None (None), residues: 0 loop : -2.85 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.009 0.001 TYR D 73 PHE 0.011 0.001 PHE D 239 TRP 0.012 0.001 TRP C 287 HIS 0.002 0.000 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 8497) covalent geometry : angle 1.15135 / 0.44 (11528) hydrogen bonds : bond 0.05139 / 3.43 ( 571) hydrogen bonds : angle 4.06581 / 2.91 ( 1701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.3252 (OUTLIER) cc_final: 0.2156 (m-10) REVERT: A 242 ARG cc_start: 0.6781 (tpp-160) cc_final: 0.5627 (pmt170) REVERT: A 243 ARG cc_start: 0.7470 (mmt180) cc_final: 0.7265 (mmt180) REVERT: A 284 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6726 (mtpp) REVERT: A 296 MET cc_start: 0.5618 (tpt) cc_final: 0.4353 (ptp) REVERT: B 73 TYR cc_start: 0.4612 (OUTLIER) cc_final: 0.3973 (m-80) REVERT: B 210 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6799 (mtm) REVERT: B 276 THR cc_start: 0.8311 (p) cc_final: 0.7787 (p) REVERT: B 286 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7708 (p) REVERT: C 106 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5916 (mp) REVERT: C 151 CYS cc_start: 0.6795 (OUTLIER) cc_final: 0.5965 (t) REVERT: D 167 PHE cc_start: 0.4028 (OUTLIER) cc_final: 0.3127 (t80) outliers start: 40 outliers final: 26 residues processed: 107 average time/residue: 0.5895 time to fit residues: 67.0910 Evaluate side-chains 111 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.215516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.145223 restraints weight = 8499.442| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.61 r_work: 0.3401 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8497 Z= 0.151 Angle : 1.157 34.423 11528 Z= 0.442 Chirality : 0.123 2.079 1318 Planarity : 0.004 0.054 1334 Dihedral : 24.075 178.259 1792 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.74 % Rotamer: Outliers : 4.69 % Allowed : 29.96 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.28), residues: 959 helix: 1.86 (0.19), residues: 765 sheet: None (None), residues: 0 loop : -2.83 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 324 TYR 0.010 0.001 TYR C 236 PHE 0.012 0.001 PHE D 239 TRP 0.013 0.001 TRP C 287 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 8497) covalent geometry : angle 1.15750 / 0.44 (11528) hydrogen bonds : bond 0.05269 / 3.52 ( 571) hydrogen bonds : angle 4.07905 / 2.92 ( 1701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.3159 (OUTLIER) cc_final: 0.2043 (m-10) REVERT: A 242 ARG cc_start: 0.6698 (tpp-160) cc_final: 0.5554 (pmt170) REVERT: A 284 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6684 (mtpp) REVERT: A 296 MET cc_start: 0.5314 (tpt) cc_final: 0.4147 (ptp) REVERT: B 73 TYR cc_start: 0.4582 (OUTLIER) cc_final: 0.3933 (m-80) REVERT: B 210 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6810 (mtm) REVERT: B 276 THR cc_start: 0.8317 (p) cc_final: 0.7848 (p) REVERT: B 286 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7738 (p) REVERT: C 85 GLU cc_start: 0.6429 (mt-10) cc_final: 0.6221 (mt-10) REVERT: C 106 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5941 (mp) REVERT: C 151 CYS cc_start: 0.6738 (OUTLIER) cc_final: 0.5900 (t) REVERT: D 167 PHE cc_start: 0.4100 (OUTLIER) cc_final: 0.3184 (t80) outliers start: 38 outliers final: 27 residues processed: 106 average time/residue: 0.6001 time to fit residues: 67.4010 Evaluate side-chains 109 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 GLN C 320 GLN D 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.211985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143229 restraints weight = 8502.440| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.65 r_work: 0.3358 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8497 Z= 0.195 Angle : 1.183 34.707 11528 Z= 0.459 Chirality : 0.124 2.069 1318 Planarity : 0.004 0.057 1334 Dihedral : 24.094 177.752 1792 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer: Outliers : 4.93 % Allowed : 29.84 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.28), residues: 959 helix: 1.74 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -2.90 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 324 TYR 0.011 0.001 TYR C 236 PHE 0.016 0.001 PHE D 239 TRP 0.022 0.001 TRP D 287 HIS 0.002 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 ( 8497) covalent geometry : angle 1.18292 / 0.46 (11528) hydrogen bonds : bond 0.05905 / 3.94 ( 571) hydrogen bonds : angle 4.19957 / 3.00 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3330.68 seconds wall clock time: 57 minutes 21.78 seconds (3441.78 seconds total)