Starting phenix.real_space_refine on Wed Jul 1 22:55:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xij_38374/07_2026/8xij_38374.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xij_38374/07_2026/8xij_38374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xij_38374/07_2026/8xij_38374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xij_38374/07_2026/8xij_38374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xij_38374/07_2026/8xij_38374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xij_38374/07_2026/8xij_38374.map" } resolution = 3.37 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= 0.000 sd= 0.037 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 17 5.16 5 C 2505 2.51 5 N 593 2.21 5 O 660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3778 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3713 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 451} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'PKZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.95, per 1000 atoms: 0.25 Number of scatterers: 3778 At special positions: 0 Unit cell: (78.1, 75.9, 73.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 3 15.00 O 660 8.00 N 593 7.00 C 2505 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: 0.21 Conformation dependent library (CDL) restraints added in 96.1 milliseconds 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 73.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 19 through 28 removed outlier: 3.908A pdb=" N ALA A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 43 removed outlier: 3.562A pdb=" N TYR A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 72 removed outlier: 3.564A pdb=" N TYR A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.963A pdb=" N THR A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 99 removed outlier: 4.097A pdb=" N CYS A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 123 through 144 removed outlier: 3.549A pdb=" N THR A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.552A pdb=" N PHE A 153 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 3.836A pdb=" N VAL A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 189 removed outlier: 3.857A pdb=" N SER A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 224 removed outlier: 3.582A pdb=" N ASN A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N THR A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASN A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 251 removed outlier: 3.557A pdb=" N SER A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Proline residue: A 246 - end of helix removed outlier: 4.202A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 261 through 278 removed outlier: 3.689A pdb=" N ALA A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.530A pdb=" N ALA A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 304 through 319 removed outlier: 4.056A pdb=" N SER A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 377 removed outlier: 3.629A pdb=" N LEU A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 416 removed outlier: 3.853A pdb=" N GLY A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 412 " --> pdb=" O TYR A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 434 removed outlier: 3.667A pdb=" N ILE A 431 " --> pdb=" O CYS A 427 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 453 removed outlier: 3.666A pdb=" N MET A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 484 removed outlier: 3.505A pdb=" N LYS A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 624 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: 0.34 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 614 1.33 - 1.45: 1057 1.45 - 1.57: 2173 1.57 - 1.69: 5 1.69 - 1.81: 25 Bond restraints: 3874 Sorted by residual: bond pdb=" O3B PKZ A 501 " pdb=" P3B PKZ A 501 " ideal model delta sigma weight residual 1.714 1.615 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O3A PKZ A 501 " pdb=" P1A PKZ A 501 " ideal model delta sigma weight residual 1.653 1.607 0.046 2.00e-02 2.50e+03 5.19e+00 bond pdb=" O5B PKZ A 501 " pdb=" P1A PKZ A 501 " ideal model delta sigma weight residual 1.648 1.606 0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" CCP PKZ A 501 " pdb=" O6A PKZ A 501 " ideal model delta sigma weight residual 1.413 1.455 -0.042 2.00e-02 2.50e+03 4.36e+00 bond pdb=" C5B PKZ A 501 " pdb=" O5B PKZ A 501 " ideal model delta sigma weight residual 1.410 1.449 -0.039 2.00e-02 2.50e+03 3.86e+00 ... (remaining 3869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 5260 3.84 - 7.68: 14 7.68 - 11.52: 2 11.52 - 15.37: 0 15.37 - 19.21: 1 Bond angle restraints: 5277 Sorted by residual: angle pdb=" C1 PKZ A 501 " pdb=" S1P PKZ A 501 " pdb=" C2P PKZ A 501 " ideal model delta sigma weight residual 101.96 121.17 -19.21 3.00e+00 1.11e-01 4.10e+01 angle pdb=" O3A PKZ A 501 " pdb=" P1A PKZ A 501 " pdb=" O5B PKZ A 501 " ideal model delta sigma weight residual 94.17 104.34 -10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CA LYS A 197 " pdb=" CB LYS A 197 " pdb=" CG LYS A 197 " ideal model delta sigma weight residual 114.10 120.76 -6.66 2.00e+00 2.50e-01 1.11e+01 angle pdb=" P1A PKZ A 501 " pdb=" O3A PKZ A 501 " pdb=" P2A PKZ A 501 " ideal model delta sigma weight residual 126.13 134.90 -8.77 3.00e+00 1.11e-01 8.55e+00 angle pdb=" CA TYR A 382 " pdb=" C TYR A 382 " pdb=" O TYR A 382 " ideal model delta sigma weight residual 121.50 118.34 3.16 1.25e+00 6.40e-01 6.40e+00 ... (remaining 5272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 2089 23.74 - 47.47: 134 47.47 - 71.21: 9 71.21 - 94.95: 3 94.95 - 118.68: 3 Dihedral angle restraints: 2238 sinusoidal: 863 harmonic: 1375 Sorted by residual: dihedral pdb=" C1 PKZ A 501 " pdb=" C2 PKZ A 501 " pdb=" C3 PKZ A 501 " pdb=" C4 PKZ A 501 " ideal model delta sinusoidal sigma weight residual 189.25 70.57 118.68 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C12 PKZ A 501 " pdb=" C10 PKZ A 501 " pdb=" C11 PKZ A 501 " pdb=" C9 PKZ A 501 " ideal model delta sinusoidal sigma weight residual 179.58 62.01 117.57 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C5 PKZ A 501 " pdb=" C6 PKZ A 501 " pdb=" C7 PKZ A 501 " pdb=" C8 PKZ A 501 " ideal model delta sinusoidal sigma weight residual 182.08 84.32 97.76 1 3.00e+01 1.11e-03 1.21e+01 ... (remaining 2235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 419 0.035 - 0.069: 161 0.069 - 0.104: 35 0.104 - 0.139: 5 0.139 - 0.173: 1 Chirality restraints: 621 Sorted by residual: chirality pdb=" C3B PKZ A 501 " pdb=" C2B PKZ A 501 " pdb=" C4B PKZ A 501 " pdb=" O3B PKZ A 501 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CB THR A 446 " pdb=" CA THR A 446 " pdb=" OG1 THR A 446 " pdb=" CG2 THR A 446 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 486 " pdb=" N ILE A 486 " pdb=" C ILE A 486 " pdb=" CB ILE A 486 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.13e-01 ... (remaining 618 not shown) Planarity restraints: 630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 123 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.10e+00 pdb=" N PRO A 124 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C7P PKZ A 501 " -0.014 2.00e-02 2.50e+03 1.14e-02 1.63e+00 pdb=" C9P PKZ A 501 " 0.007 2.00e-02 2.50e+03 pdb=" CAP PKZ A 501 " -0.012 2.00e-02 2.50e+03 pdb=" N8P PKZ A 501 " 0.016 2.00e-02 2.50e+03 pdb=" O9P PKZ A 501 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 357 " 0.018 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO A 358 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " 0.016 5.00e-02 4.00e+02 ... (remaining 627 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 341 2.74 - 3.28: 3708 3.28 - 3.82: 5707 3.82 - 4.36: 6226 4.36 - 4.90: 11433 Nonbonded interactions: 27415 Sorted by model distance: nonbonded pdb=" OG SER A 162 " pdb=" OD2 ASP A 165 " model vdw 2.203 3.040 nonbonded pdb=" O SER A 179 " pdb=" OG SER A 179 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASP A 58 " pdb=" ND2 ASN A 62 " model vdw 2.287 3.120 nonbonded pdb=" O ASP A 290 " pdb=" OG SER A 296 " model vdw 2.326 3.040 nonbonded pdb=" OE2 GLU A 22 " pdb=" NH2 ARG A 152 " model vdw 2.341 3.120 ... (remaining 27410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.380 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.320 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 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 : 0.004 0.099 3874 Z= 0.193 Angle : 0.695 19.207 5277 Z= 0.354 Chirality : 0.039 0.173 621 Planarity : 0.003 0.036 630 Dihedral : 15.235 118.685 1350 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 12.65 % Favored : 87.35 % 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: 1.55 (0.42), residues: 463 helix: 1.60 (0.31), residues: 328 sheet: None (None), residues: 0 loop : -0.31 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 216 TYR 0.011 0.001 TYR A 129 PHE 0.011 0.001 PHE A 149 TRP 0.009 0.001 TRP A 350 HIS 0.001 0.000 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 ( 3874) covalent geometry : angle 0.69525 / 0.35 ( 5277) hydrogen bonds : bond 0.15360 / 10.21 ( 209) hydrogen bonds : angle 4.13076 / 3.03 ( 624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.132 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0586 time to fit residues: 3.1309 Evaluate side-chains 42 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.0070 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.154475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112150 restraints weight = 4716.949| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.43 r_work: 0.3139 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3874 Z= 0.124 Angle : 0.478 5.386 5277 Z= 0.244 Chirality : 0.038 0.119 621 Planarity : 0.004 0.034 630 Dihedral : 9.419 98.821 528 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.41 % Allowed : 9.98 % Favored : 86.62 % 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: 1.69 (0.42), residues: 463 helix: 1.68 (0.31), residues: 333 sheet: None (None), residues: 0 loop : -0.25 (0.56), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 216 TYR 0.013 0.001 TYR A 470 PHE 0.010 0.001 PHE A 149 TRP 0.006 0.001 TRP A 63 HIS 0.000 0.000 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 3874) covalent geometry : angle 0.47819 / 0.24 ( 5277) hydrogen bonds : bond 0.05761 / 3.76 ( 209) hydrogen bonds : angle 3.43611 / 2.61 ( 624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.138 Fit side-chains REVERT: A 376 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7461 (t) outliers start: 14 outliers final: 10 residues processed: 50 average time/residue: 0.0631 time to fit residues: 4.1212 Evaluate side-chains 50 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110905 restraints weight = 4729.282| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.43 r_work: 0.3123 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3874 Z= 0.126 Angle : 0.469 4.895 5277 Z= 0.238 Chirality : 0.038 0.116 621 Planarity : 0.003 0.035 630 Dihedral : 8.122 71.117 528 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.65 % Allowed : 11.44 % Favored : 84.91 % 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: 1.69 (0.42), residues: 463 helix: 1.71 (0.31), residues: 333 sheet: None (None), residues: 0 loop : -0.34 (0.55), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 216 TYR 0.014 0.001 TYR A 470 PHE 0.011 0.001 PHE A 149 TRP 0.005 0.001 TRP A 350 HIS 0.000 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 3874) covalent geometry : angle 0.46887 / 0.24 ( 5277) hydrogen bonds : bond 0.05769 / 3.78 ( 209) hydrogen bonds : angle 3.33531 / 2.53 ( 624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.082 Fit side-chains REVERT: A 76 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: A 197 LYS cc_start: 0.7229 (tptm) cc_final: 0.6953 (tptp) outliers start: 15 outliers final: 12 residues processed: 52 average time/residue: 0.0419 time to fit residues: 2.8267 Evaluate side-chains 53 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.153816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111887 restraints weight = 4685.813| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.43 r_work: 0.3139 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3874 Z= 0.117 Angle : 0.452 4.879 5277 Z= 0.230 Chirality : 0.037 0.127 621 Planarity : 0.003 0.035 630 Dihedral : 7.582 64.561 528 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.65 % Allowed : 12.65 % Favored : 83.70 % 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: 1.81 (0.42), residues: 463 helix: 1.81 (0.31), residues: 331 sheet: None (None), residues: 0 loop : -0.30 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 257 TYR 0.013 0.001 TYR A 470 PHE 0.010 0.001 PHE A 149 TRP 0.005 0.001 TRP A 314 HIS 0.000 0.000 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 3874) covalent geometry : angle 0.45200 / 0.23 ( 5277) hydrogen bonds : bond 0.05359 / 3.50 ( 209) hydrogen bonds : angle 3.30819 / 2.53 ( 624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.144 Fit side-chains REVERT: A 76 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7915 (pm20) outliers start: 15 outliers final: 12 residues processed: 50 average time/residue: 0.0679 time to fit residues: 4.3558 Evaluate side-chains 53 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.0170 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.0370 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.153763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.111126 restraints weight = 4746.094| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.47 r_work: 0.3135 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3874 Z= 0.113 Angle : 0.447 4.872 5277 Z= 0.227 Chirality : 0.037 0.132 621 Planarity : 0.003 0.035 630 Dihedral : 7.226 62.951 528 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.41 % Allowed : 13.63 % Favored : 82.97 % 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: 1.87 (0.42), residues: 463 helix: 1.85 (0.31), residues: 331 sheet: None (None), residues: 0 loop : -0.28 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 257 TYR 0.012 0.001 TYR A 470 PHE 0.010 0.001 PHE A 149 TRP 0.005 0.001 TRP A 314 HIS 0.000 0.000 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 3874) covalent geometry : angle 0.44684 / 0.23 ( 5277) hydrogen bonds : bond 0.05191 / 3.39 ( 209) hydrogen bonds : angle 3.24444 / 2.48 ( 624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.134 Fit side-chains REVERT: A 76 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7940 (pm20) outliers start: 14 outliers final: 12 residues processed: 50 average time/residue: 0.0657 time to fit residues: 4.2166 Evaluate side-chains 54 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.0010 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.152020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109814 restraints weight = 4768.181| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.46 r_work: 0.3108 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3874 Z= 0.140 Angle : 0.480 4.929 5277 Z= 0.244 Chirality : 0.038 0.133 621 Planarity : 0.003 0.038 630 Dihedral : 7.343 63.335 528 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.65 % Allowed : 14.11 % Favored : 82.24 % 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: 1.66 (0.42), residues: 463 helix: 1.69 (0.31), residues: 334 sheet: None (None), residues: 0 loop : -0.41 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 257 TYR 0.014 0.001 TYR A 470 PHE 0.011 0.001 PHE A 312 TRP 0.007 0.001 TRP A 350 HIS 0.000 0.000 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 3874) covalent geometry : angle 0.47992 / 0.24 ( 5277) hydrogen bonds : bond 0.06016 / 3.93 ( 209) hydrogen bonds : angle 3.34282 / 2.56 ( 624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7945 (pm20) outliers start: 15 outliers final: 13 residues processed: 52 average time/residue: 0.0556 time to fit residues: 3.7199 Evaluate side-chains 55 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 31 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.154774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112773 restraints weight = 4729.805| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.47 r_work: 0.3145 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3874 Z= 0.110 Angle : 0.453 6.038 5277 Z= 0.229 Chirality : 0.037 0.140 621 Planarity : 0.003 0.036 630 Dihedral : 6.795 57.677 528 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.16 % Allowed : 15.33 % Favored : 81.51 % 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: 1.85 (0.42), residues: 463 helix: 1.83 (0.31), residues: 332 sheet: None (None), residues: 0 loop : -0.28 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.012 0.001 TYR A 470 PHE 0.009 0.001 PHE A 149 TRP 0.005 0.001 TRP A 314 HIS 0.000 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 3874) covalent geometry : angle 0.45269 / 0.23 ( 5277) hydrogen bonds : bond 0.04949 / 3.23 ( 209) hydrogen bonds : angle 3.22129 / 2.47 ( 624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.084 Fit side-chains REVERT: A 76 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7899 (pm20) outliers start: 13 outliers final: 12 residues processed: 49 average time/residue: 0.0649 time to fit residues: 3.9429 Evaluate side-chains 53 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 0.0670 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.156674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116712 restraints weight = 4595.578| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.33 r_work: 0.3185 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3874 Z= 0.101 Angle : 0.437 4.867 5277 Z= 0.220 Chirality : 0.037 0.140 621 Planarity : 0.003 0.035 630 Dihedral : 6.396 56.006 528 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.41 % Allowed : 15.33 % Favored : 81.27 % 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 (0.41), residues: 463 helix: 1.91 (0.31), residues: 332 sheet: None (None), residues: 0 loop : -0.30 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.011 0.001 TYR A 470 PHE 0.008 0.001 PHE A 149 TRP 0.005 0.001 TRP A 314 HIS 0.000 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 3874) covalent geometry : angle 0.43681 / 0.22 ( 5277) hydrogen bonds : bond 0.04535 / 2.97 ( 209) hydrogen bonds : angle 3.17034 / 2.43 ( 624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.139 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 52 average time/residue: 0.0609 time to fit residues: 4.1022 Evaluate side-chains 57 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.152355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111097 restraints weight = 4702.277| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.41 r_work: 0.3170 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3874 Z= 0.105 Angle : 0.441 4.869 5277 Z= 0.222 Chirality : 0.037 0.143 621 Planarity : 0.003 0.035 630 Dihedral : 6.099 49.221 528 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.41 % Allowed : 15.33 % Favored : 81.27 % 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: 1.94 (0.41), residues: 463 helix: 1.93 (0.30), residues: 332 sheet: None (None), residues: 0 loop : -0.34 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.011 0.001 TYR A 470 PHE 0.009 0.001 PHE A 149 TRP 0.005 0.001 TRP A 314 HIS 0.000 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 3874) covalent geometry : angle 0.44101 / 0.22 ( 5277) hydrogen bonds : bond 0.04696 / 3.07 ( 209) hydrogen bonds : angle 3.17580 / 2.43 ( 624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.083 Fit side-chains REVERT: A 76 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8022 (pm20) outliers start: 14 outliers final: 13 residues processed: 47 average time/residue: 0.0497 time to fit residues: 2.9958 Evaluate side-chains 53 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.151405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110815 restraints weight = 4734.914| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.36 r_work: 0.3118 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3874 Z= 0.141 Angle : 0.485 4.936 5277 Z= 0.245 Chirality : 0.038 0.139 621 Planarity : 0.003 0.038 630 Dihedral : 5.848 51.625 528 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.65 % Allowed : 15.33 % Favored : 81.02 % 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: 1.78 (0.41), residues: 463 helix: 1.82 (0.30), residues: 332 sheet: None (None), residues: 0 loop : -0.42 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.014 0.001 TYR A 470 PHE 0.011 0.001 PHE A 149 TRP 0.007 0.001 TRP A 37 HIS 0.001 0.000 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 3874) covalent geometry : angle 0.48460 / 0.24 ( 5277) hydrogen bonds : bond 0.05920 / 3.87 ( 209) hydrogen bonds : angle 3.29205 / 2.52 ( 624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.096 Fit side-chains REVERT: A 76 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8050 (pm20) outliers start: 15 outliers final: 14 residues processed: 49 average time/residue: 0.0586 time to fit residues: 3.6579 Evaluate side-chains 54 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 43 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.158457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117601 restraints weight = 4844.758| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.42 r_work: 0.2781 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3874 Z= 0.126 Angle : 0.467 4.895 5277 Z= 0.236 Chirality : 0.038 0.141 621 Planarity : 0.003 0.037 630 Dihedral : 5.798 51.315 528 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.65 % Allowed : 15.57 % Favored : 80.78 % 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 (0.41), residues: 463 helix: 1.87 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -0.36 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.013 0.001 TYR A 470 PHE 0.010 0.001 PHE A 149 TRP 0.005 0.001 TRP A 37 HIS 0.000 0.000 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 3874) covalent geometry : angle 0.46720 / 0.24 ( 5277) hydrogen bonds : bond 0.05534 / 3.62 ( 209) hydrogen bonds : angle 3.25004 / 2.49 ( 624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 925.63 seconds wall clock time: 16 minutes 30.38 seconds (990.38 seconds total)