Starting phenix.real_space_refine on Fri Sep 11 07:39:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24vp_69847/09_2026/24vp_69847.cif Found real_map, /net/cci-nas-00/data/ceres_data/24vp_69847/09_2026/24vp_69847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/24vp_69847/09_2026/24vp_69847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24vp_69847/09_2026/24vp_69847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/24vp_69847/09_2026/24vp_69847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24vp_69847/09_2026/24vp_69847.map" } resolution = 3.26 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= 0.114 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 11 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: 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: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 81 Unusual residues: {'YJ0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.14, per 1000 atoms: 0.26 Number of scatterers: 8264 At special positions: 0 Unit cell: (82.9521, 106.653, 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: 0.79 Conformation dependent library (CDL) restraints added in 484.5 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 81.1% 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 112 through 117 removed outlier: 3.702A pdb=" N ARG A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 143 removed outlier: 3.552A pdb=" N LEU A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.875A 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 239 removed outlier: 3.953A pdb=" N GLN A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 257 removed outlier: 3.866A pdb=" N HIS A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 283 removed outlier: 3.680A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 326 through 345 removed outlier: 3.789A pdb=" N ALA A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 366 Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 91 through 114 removed outlier: 3.762A pdb=" N HIS B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 147 Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.521A pdb=" N LEU B 160 " --> pdb=" O TRP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 200 through 209 removed outlier: 4.095A pdb=" N ILE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 227 through 253 removed outlier: 3.687A pdb=" N VAL B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 305 removed outlier: 3.657A pdb=" N ALA B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 326 removed outlier: 3.843A pdb=" N GLY B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.816A 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: 4.356A pdb=" N HIS C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 118 removed outlier: 6.144A pdb=" N GLU C 116 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 118 " --> pdb=" O LYS C 115 " (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 163 Processing helix chain 'C' and resid 165 through 183 Processing helix chain 'C' and resid 201 through 209 removed outlier: 3.961A 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 230 through 253 Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 288 through 326 removed outlier: 4.186A pdb=" N LEU C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Proline residue: C 307 - end of helix removed outlier: 3.641A pdb=" N LYS C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 93 through 113 Processing helix chain 'D' and resid 118 through 145 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: 4.088A 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 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.788A pdb=" N ALA D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 326 581 hydrogen bonds defined for protein. 1740 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: 1.25 Time building geometry restraints manager: 1.05 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: 1161 1.31 - 1.43: 2557 1.43 - 1.56: 4721 1.56 - 1.69: 8 1.69 - 1.81: 50 Bond restraints: 8497 Sorted by residual: bond pdb=" C21 9PE A1001 " pdb=" O21 9PE A1001 " ideal model delta sigma weight residual 1.329 1.465 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C31 9PE A1001 " pdb=" O31 9PE A1001 " ideal model delta sigma weight residual 1.325 1.459 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C31 9PE C 602 " pdb=" O31 9PE C 602 " 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 1.398 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C21 9PE B 602 " pdb=" O21 9PE B 602 " ideal model delta sigma weight residual 1.329 1.400 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 8492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 11167 2.35 - 4.71: 223 4.71 - 7.06: 96 7.06 - 9.41: 31 9.41 - 11.77: 11 Bond angle restraints: 11528 Sorted by residual: angle pdb=" C LEU A 229 " pdb=" CA LEU A 229 " pdb=" CB LEU A 229 " ideal model delta sigma weight residual 117.23 110.27 6.96 1.36e+00 5.41e-01 2.62e+01 angle pdb=" N LEU D 199 " pdb=" CA LEU D 199 " pdb=" C LEU D 199 " ideal model delta sigma weight residual 114.56 108.41 6.15 1.27e+00 6.20e-01 2.35e+01 angle pdb=" N ASP B 171 " pdb=" CA ASP B 171 " pdb=" C ASP B 171 " ideal model delta sigma weight residual 111.03 106.39 4.64 1.11e+00 8.12e-01 1.75e+01 angle pdb=" C ARG B 88 " pdb=" CA ARG B 88 " pdb=" CB ARG B 88 " ideal model delta sigma weight residual 116.34 110.57 5.77 1.40e+00 5.10e-01 1.70e+01 angle pdb=" N ILE D 93 " pdb=" CA ILE D 93 " pdb=" C ILE D 93 " ideal model delta sigma weight residual 111.62 108.38 3.24 7.90e-01 1.60e+00 1.68e+01 ... (remaining 11523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 4815 35.98 - 71.95: 317 71.95 - 107.93: 112 107.93 - 143.90: 71 143.90 - 179.88: 26 Dihedral angle restraints: 5341 sinusoidal: 2528 harmonic: 2813 Sorted by residual: dihedral pdb=" N 9PE B 602 " pdb=" C11 9PE B 602 " pdb=" C12 9PE B 602 " pdb=" O13 9PE B 602 " ideal model delta sinusoidal sigma weight residual -66.84 113.04 -179.88 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O30 YJ0 D 601 " pdb=" C31 YJ0 D 601 " pdb=" C32 YJ0 D 601 " pdb=" O52 YJ0 D 601 " ideal model delta sinusoidal sigma weight residual 234.92 58.44 176.48 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C37 YJ0 C 601 " pdb=" C34 YJ0 C 601 " pdb=" C35 YJ0 C 601 " pdb=" O39 YJ0 C 601 " ideal model delta sinusoidal sigma weight residual -67.37 106.60 -173.97 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.216: 1284 1.216 - 2.431: 0 2.431 - 3.647: 0 3.647 - 4.862: 5 4.862 - 6.078: 29 Chirality restraints: 1318 Sorted by residual: chirality pdb=" C12 YJ0 D 601 " pdb=" C11 YJ0 D 601 " pdb=" C13 YJ0 D 601 " pdb=" C7 YJ0 D 601 " both_signs ideal model delta sigma weight residual False 3.10 -2.98 6.08 2.00e-01 2.50e+01 9.23e+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 9.14e+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 2.74 -5.61 2.00e-01 2.50e+01 7.86e+02 ... (remaining 1315 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 C 601 " -0.165 2.00e-02 2.50e+03 1.39e-01 2.40e+02 pdb=" C18 YJ0 C 601 " 0.201 2.00e-02 2.50e+03 pdb=" C19 YJ0 C 601 " 0.094 2.00e-02 2.50e+03 pdb=" C20 YJ0 C 601 " 0.009 2.00e-02 2.50e+03 pdb=" C24 YJ0 C 601 " -0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 D 601 " 0.107 2.00e-02 2.50e+03 8.85e-02 9.80e+01 pdb=" C18 YJ0 D 601 " -0.131 2.00e-02 2.50e+03 pdb=" C19 YJ0 D 601 " -0.052 2.00e-02 2.50e+03 pdb=" C20 YJ0 D 601 " -0.011 2.00e-02 2.50e+03 pdb=" C24 YJ0 D 601 " 0.088 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 5.60e+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: 2.23 - 2.76: 1508 2.76 - 3.30: 7921 3.30 - 3.83: 13856 3.83 - 4.37: 14991 4.37 - 4.90: 26521 Nonbonded interactions: 64797 Sorted by model distance: nonbonded pdb=" O ARG C 74 " pdb=" NE2 GLN C 77 " model vdw 2.227 3.120 nonbonded pdb=" OH TYR B 94 " pdb=" OE1 GLU B 139 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR C 94 " pdb=" OE1 GLU C 139 " model vdw 2.272 3.040 nonbonded pdb=" NH1 ARG B 212 " pdb=" O3 YJ0 B 601 " model vdw 2.273 3.120 nonbonded pdb=" OG1 THR A 313 " pdb=" OH TYR B 279 " model vdw 2.273 3.040 ... (remaining 64792 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 601) selection = (chain 'C' and (resid 70 through 182 or resid 197 through 601)) selection = (chain 'D' and (resid 70 through 182 or resid 197 through 601)) } 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: 0.880 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.590 Find NCS groups from input model: 0.170 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 0.136 8497 Z= 0.263 Angle : 0.994 11.767 11528 Z= 0.425 Chirality : 0.835 6.078 1318 Planarity : 0.006 0.139 1334 Dihedral : 33.710 179.877 3545 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.94 % Favored : 93.85 % Rotamer: Outliers : 0.49 % Allowed : 28.48 % Favored : 71.02 % 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: 1.45 (0.28), residues: 959 helix: 1.93 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -2.83 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 117 TYR 0.027 0.001 TYR D 153 PHE 0.021 0.001 PHE B 136 TRP 0.022 0.001 TRP C 287 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.26 ( 8497) covalent geometry : angle 0.99360 / 0.43 (11528) hydrogen bonds : bond 0.11973 / 8.86 ( 581) hydrogen bonds : angle 4.96762 / 3.66 ( 1740) *********************** 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 133 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 LYS cc_start: 0.6753 (tmtt) cc_final: 0.6491 (tptm) REVERT: C 318 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8457 (ttpt) REVERT: D 254 LYS cc_start: 0.7139 (tptp) cc_final: 0.6485 (mttm) outliers start: 4 outliers final: 2 residues processed: 132 average time/residue: 0.1288 time to fit residues: 21.7659 Evaluate side-chains 128 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain C residue 253 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.211771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139189 restraints weight = 9140.626| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.59 r_work: 0.3293 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8497 Z= 0.154 Angle : 1.234 35.204 11528 Z= 0.466 Chirality : 0.129 2.206 1318 Planarity : 0.004 0.061 1334 Dihedral : 27.994 179.864 1794 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.32 % Favored : 94.58 % Rotamer: Outliers : 2.71 % Allowed : 27.13 % Favored : 70.16 % 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: 1.58 (0.28), residues: 959 helix: 1.97 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -2.84 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 117 TYR 0.017 0.001 TYR D 73 PHE 0.014 0.001 PHE D 99 TRP 0.016 0.001 TRP A 327 HIS 0.006 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 8497) covalent geometry : angle 1.23368 / 0.47 (11528) hydrogen bonds : bond 0.05282 / 3.47 ( 581) hydrogen bonds : angle 4.18293 / 3.10 ( 1740) *********************** 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 155 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 PHE cc_start: 0.7939 (m-80) cc_final: 0.7639 (m-80) REVERT: B 175 LEU cc_start: 0.8601 (tp) cc_final: 0.8363 (tp) REVERT: B 212 ARG cc_start: 0.6771 (mtt90) cc_final: 0.6516 (mtt90) REVERT: B 229 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8410 (tttm) REVERT: C 164 ARG cc_start: 0.6956 (mtp-110) cc_final: 0.6670 (mtp85) REVERT: C 318 LYS cc_start: 0.8501 (ttpp) cc_final: 0.8182 (ttpt) REVERT: D 254 LYS cc_start: 0.7833 (tptp) cc_final: 0.6617 (mtpp) outliers start: 22 outliers final: 10 residues processed: 151 average time/residue: 0.1306 time to fit residues: 25.1788 Evaluate side-chains 138 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.207836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143235 restraints weight = 9136.724| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.16 r_work: 0.3276 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8497 Z= 0.184 Angle : 1.193 33.603 11528 Z= 0.457 Chirality : 0.128 2.180 1318 Planarity : 0.004 0.053 1334 Dihedral : 25.957 177.749 1791 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer: Outliers : 3.45 % Allowed : 26.26 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.53 (0.28), residues: 959 helix: 1.89 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -2.71 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 117 TYR 0.016 0.001 TYR D 73 PHE 0.015 0.001 PHE B 92 TRP 0.017 0.001 TRP A 327 HIS 0.007 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 8497) covalent geometry : angle 1.19335 / 0.46 (11528) hydrogen bonds : bond 0.05628 / 3.66 ( 581) hydrogen bonds : angle 4.19053 / 3.12 ( 1740) *********************** 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 157 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8901 (mp0) cc_final: 0.8622 (mp0) REVERT: B 175 LEU cc_start: 0.8698 (tp) cc_final: 0.8427 (tp) REVERT: B 212 ARG cc_start: 0.7043 (mtt90) cc_final: 0.6802 (mtt90) REVERT: B 229 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8562 (tttm) REVERT: C 318 LYS cc_start: 0.8619 (ttpp) cc_final: 0.8389 (ttpt) REVERT: D 122 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7592 (mt-10) REVERT: D 254 LYS cc_start: 0.7944 (tptp) cc_final: 0.6692 (mtpp) REVERT: D 306 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8464 (mp) REVERT: D 324 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7576 (mtt90) outliers start: 28 outliers final: 16 residues processed: 150 average time/residue: 0.1161 time to fit residues: 22.8132 Evaluate side-chains 139 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 324 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 92 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.209521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145469 restraints weight = 9260.160| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.15 r_work: 0.3302 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8497 Z= 0.152 Angle : 1.165 33.155 11528 Z= 0.442 Chirality : 0.125 2.103 1318 Planarity : 0.004 0.039 1334 Dihedral : 25.161 178.578 1790 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.63 % Favored : 94.26 % Rotamer: Outliers : 3.70 % Allowed : 27.00 % Favored : 69.30 % 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: 1.64 (0.27), residues: 959 helix: 1.96 (0.18), residues: 765 sheet: None (None), residues: 0 loop : -2.64 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.021 0.001 TYR D 81 PHE 0.010 0.001 PHE B 136 TRP 0.015 0.001 TRP C 287 HIS 0.007 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 8497) covalent geometry : angle 1.16485 / 0.44 (11528) hydrogen bonds : bond 0.05195 / 3.37 ( 581) hydrogen bonds : angle 4.12430 / 3.07 ( 1740) *********************** 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 161 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: B 175 LEU cc_start: 0.8693 (tp) cc_final: 0.8423 (tp) REVERT: B 212 ARG cc_start: 0.7004 (mtt90) cc_final: 0.6646 (mtt180) REVERT: C 210 MET cc_start: 0.6840 (ptp) cc_final: 0.6615 (ptp) REVERT: C 318 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8399 (ttpt) REVERT: D 122 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7548 (mt-10) REVERT: D 254 LYS cc_start: 0.7947 (tptp) cc_final: 0.6584 (mtpp) outliers start: 30 outliers final: 20 residues processed: 156 average time/residue: 0.1173 time to fit residues: 23.3509 Evaluate side-chains 148 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 207 MET 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: 0.9990 chunk 73 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4308 r_free = 0.4308 target = 0.212122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.146377 restraints weight = 9282.426| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.24 r_work: 0.3318 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8497 Z= 0.139 Angle : 1.157 32.900 11528 Z= 0.438 Chirality : 0.125 2.090 1318 Planarity : 0.004 0.055 1334 Dihedral : 24.761 179.926 1790 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.06 % Rotamer: Outliers : 3.70 % Allowed : 27.00 % Favored : 69.30 % 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: 1.76 (0.28), residues: 959 helix: 2.04 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -2.59 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 117 TYR 0.014 0.001 TYR D 81 PHE 0.010 0.001 PHE B 136 TRP 0.017 0.001 TRP C 287 HIS 0.005 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 8497) covalent geometry : angle 1.15699 / 0.44 (11528) hydrogen bonds : bond 0.04999 / 3.23 ( 581) hydrogen bonds : angle 4.03533 / 3.01 ( 1740) *********************** 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 160 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.5402 (mmm-85) cc_final: 0.5086 (tpp-160) REVERT: A 343 PHE cc_start: 0.8165 (m-80) cc_final: 0.7824 (m-80) REVERT: B 175 LEU cc_start: 0.8685 (tp) cc_final: 0.8410 (tp) REVERT: C 318 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8289 (ttpt) REVERT: D 122 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7599 (mt-10) REVERT: D 253 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7766 (mt-10) REVERT: D 254 LYS cc_start: 0.7950 (tptp) cc_final: 0.6554 (mtpp) REVERT: D 306 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8386 (mp) REVERT: D 324 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7504 (mtt90) outliers start: 30 outliers final: 22 residues processed: 156 average time/residue: 0.1214 time to fit residues: 24.3640 Evaluate side-chains 150 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 326 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4280 r_free = 0.4280 target = 0.208971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141518 restraints weight = 9154.900| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.27 r_work: 0.3258 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8497 Z= 0.181 Angle : 1.176 33.132 11528 Z= 0.451 Chirality : 0.124 2.067 1318 Planarity : 0.004 0.041 1334 Dihedral : 24.485 179.516 1790 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.74 % Rotamer: Outliers : 4.56 % Allowed : 26.26 % Favored : 69.17 % 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: 1.71 (0.27), residues: 959 helix: 2.01 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -2.56 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 209 TYR 0.019 0.001 TYR D 81 PHE 0.010 0.001 PHE D 239 TRP 0.017 0.001 TRP C 287 HIS 0.006 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 8497) covalent geometry : angle 1.17592 / 0.45 (11528) hydrogen bonds : bond 0.05518 / 3.59 ( 581) hydrogen bonds : angle 4.10750 / 3.07 ( 1740) *********************** 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 169 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.4413 (tpt170) REVERT: B 175 LEU cc_start: 0.8736 (tp) cc_final: 0.8477 (tp) REVERT: C 100 LEU cc_start: 0.7956 (mt) cc_final: 0.7690 (tp) REVERT: C 318 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8526 (ttpt) REVERT: D 122 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7562 (mt-10) REVERT: D 253 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7853 (mt-10) REVERT: D 306 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8429 (mp) REVERT: D 324 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7549 (mtt90) outliers start: 37 outliers final: 27 residues processed: 161 average time/residue: 0.1230 time to fit residues: 25.5605 Evaluate side-chains 156 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 326 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 0.0870 chunk 80 optimal weight: 9.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.212137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146486 restraints weight = 9307.288| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.24 r_work: 0.3314 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1909 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= 0.134 Angle : 1.153 32.675 11528 Z= 0.437 Chirality : 0.124 2.059 1318 Planarity : 0.004 0.041 1334 Dihedral : 24.132 179.792 1790 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.05 % Favored : 93.85 % Rotamer: Outliers : 3.58 % Allowed : 27.25 % Favored : 69.17 % 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: 1.86 (0.28), residues: 959 helix: 2.10 (0.19), residues: 765 sheet: None (None), residues: 0 loop : -2.48 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 209 TYR 0.021 0.001 TYR D 81 PHE 0.008 0.001 PHE B 136 TRP 0.018 0.001 TRP C 287 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 8497) covalent geometry : angle 1.15270 / 0.44 (11528) hydrogen bonds : bond 0.04951 / 3.21 ( 581) hydrogen bonds : angle 4.01613 / 3.00 ( 1740) *********************** 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 160 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.4350 (tpt170) REVERT: A 288 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6533 (tt0) REVERT: A 343 PHE cc_start: 0.8179 (m-80) cc_final: 0.7844 (m-80) REVERT: B 175 LEU cc_start: 0.8727 (tp) cc_final: 0.8465 (tp) REVERT: C 219 LEU cc_start: 0.8559 (tp) cc_final: 0.8288 (tp) REVERT: C 318 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8423 (ttpt) REVERT: D 253 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7838 (mt-10) REVERT: D 306 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8376 (mp) REVERT: D 324 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.6474 (tmm160) outliers start: 29 outliers final: 19 residues processed: 155 average time/residue: 0.1255 time to fit residues: 24.8710 Evaluate side-chains 151 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 326 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 31 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.208754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144081 restraints weight = 9159.444| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.19 r_work: 0.3289 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8497 Z= 0.154 Angle : 1.163 32.822 11528 Z= 0.444 Chirality : 0.123 2.053 1318 Planarity : 0.004 0.040 1334 Dihedral : 23.923 179.866 1790 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.53 % Rotamer: Outliers : 3.82 % Allowed : 27.00 % Favored : 69.17 % 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: 1.82 (0.28), residues: 959 helix: 2.07 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -2.49 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 209 TYR 0.021 0.001 TYR D 81 PHE 0.009 0.001 PHE B 92 TRP 0.020 0.001 TRP C 287 HIS 0.005 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 8497) covalent geometry : angle 1.16255 / 0.44 (11528) hydrogen bonds : bond 0.05208 / 3.38 ( 581) hydrogen bonds : angle 4.05982 / 3.03 ( 1740) *********************** 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 164 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 LEU cc_start: 0.8699 (tp) cc_final: 0.8457 (tp) REVERT: C 318 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8429 (ttpt) REVERT: D 253 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7830 (mt-10) REVERT: D 306 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8417 (mp) REVERT: D 324 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7527 (mtt90) outliers start: 31 outliers final: 26 residues processed: 156 average time/residue: 0.1211 time to fit residues: 24.1805 Evaluate side-chains 157 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 253 GLU 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 C residue 84 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 326 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.210867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145384 restraints weight = 9258.998| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.24 r_work: 0.3300 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8497 Z= 0.150 Angle : 1.160 32.798 11528 Z= 0.443 Chirality : 0.123 2.047 1318 Planarity : 0.004 0.042 1334 Dihedral : 23.726 179.983 1790 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer: Outliers : 3.82 % Allowed : 27.37 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.28), residues: 959 helix: 2.13 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -2.50 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 209 TYR 0.021 0.001 TYR D 81 PHE 0.008 0.001 PHE D 296 TRP 0.022 0.001 TRP C 287 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 8497) covalent geometry : angle 1.16001 / 0.44 (11528) hydrogen bonds : bond 0.05105 / 3.31 ( 581) hydrogen bonds : angle 4.04825 / 3.02 ( 1740) *********************** 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 165 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 LEU cc_start: 0.8667 (tp) cc_final: 0.8434 (tp) REVERT: B 325 GLN cc_start: 0.7359 (pp30) cc_final: 0.5916 (mt0) REVERT: D 306 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8385 (mp) REVERT: D 324 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6493 (tmm160) outliers start: 31 outliers final: 26 residues processed: 158 average time/residue: 0.1251 time to fit residues: 25.5075 Evaluate side-chains 158 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 253 GLU 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 C residue 84 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 326 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 0.0770 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.211052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.146304 restraints weight = 9150.127| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.06 r_work: 0.3335 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8497 Z= 0.141 Angle : 1.157 32.632 11528 Z= 0.442 Chirality : 0.123 2.044 1318 Planarity : 0.004 0.043 1334 Dihedral : 23.178 179.808 1790 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.53 % Rotamer: Outliers : 3.82 % Allowed : 27.25 % Favored : 68.93 % 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: 1.93 (0.28), residues: 959 helix: 2.16 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -2.47 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 86 TYR 0.021 0.001 TYR D 81 PHE 0.009 0.001 PHE C 136 TRP 0.021 0.001 TRP C 287 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 8497) covalent geometry : angle 1.15744 / 0.44 (11528) hydrogen bonds : bond 0.04916 / 3.18 ( 581) hydrogen bonds : angle 4.01669 / 3.00 ( 1740) ********************** 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 166 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.4579 (tpt170) REVERT: A 242 ARG cc_start: 0.7904 (ptp90) cc_final: 0.7616 (ptp90) REVERT: A 343 PHE cc_start: 0.8176 (m-80) cc_final: 0.7851 (m-80) REVERT: C 86 ARG cc_start: 0.8025 (mpp80) cc_final: 0.7718 (mpp80) REVERT: C 197 ARG cc_start: 0.3183 (OUTLIER) cc_final: 0.2708 (ptt-90) REVERT: C 318 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8435 (ttpt) REVERT: D 122 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7283 (mm-30) REVERT: D 253 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7634 (mt-10) REVERT: D 306 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8383 (mp) REVERT: D 324 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6573 (tmm160) outliers start: 31 outliers final: 23 residues processed: 161 average time/residue: 0.1270 time to fit residues: 25.9893 Evaluate side-chains 157 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain B residue 253 GLU 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 C residue 84 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 326 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 0.0060 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 31 optimal weight: 0.0040 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 84 optimal weight: 0.0670 overall best weight: 0.3146 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.215343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149727 restraints weight = 9250.811| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.23 r_work: 0.3366 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8497 Z= 0.125 Angle : 1.146 32.423 11528 Z= 0.434 Chirality : 0.123 2.047 1318 Planarity : 0.004 0.043 1334 Dihedral : 22.886 179.982 1790 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.94 % Favored : 93.95 % Rotamer: Outliers : 2.84 % Allowed : 28.36 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.28), residues: 959 helix: 2.31 (0.19), residues: 753 sheet: None (None), residues: 0 loop : -2.53 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 206 TYR 0.022 0.001 TYR D 81 PHE 0.009 0.001 PHE C 136 TRP 0.020 0.001 TRP C 287 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 8497) covalent geometry : angle 1.14579 / 0.43 (11528) hydrogen bonds : bond 0.04530 / 2.92 ( 581) hydrogen bonds : angle 3.96585 / 2.96 ( 1740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.43 seconds wall clock time: 47 minutes 18.25 seconds (2838.25 seconds total)