Starting phenix.real_space_refine on Wed Jul 1 23:19:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uv0_26808/07_2026/7uv0_26808.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uv0_26808/07_2026/7uv0_26808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uv0_26808/07_2026/7uv0_26808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uv0_26808/07_2026/7uv0_26808.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uv0_26808/07_2026/7uv0_26808.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uv0_26808/07_2026/7uv0_26808.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uv0_26808/07_2026/7uv0_26808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uv0_26808/07_2026/7uv0_26808.map" } resolution = 3.1 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= 0.001 sd= 0.081 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: 7 Type Number sf(0) Gaussians I 1 10.91 5 P 1 5.49 5 S 27 5.16 5 Na 2 4.78 5 C 2494 2.51 5 N 594 2.21 5 O 665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3739 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 24, 'TRANS': 476} Chain breaks: 3 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {' NA': 2, '3PH': 1, 'IOD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 1.02, per 1000 atoms: 0.27 Number of scatterers: 3784 At special positions: 0 Unit cell: (67.284, 85.44, 83.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) I 1 52.95 S 27 16.00 P 1 15.00 Na 2 11.00 O 665 8.00 N 594 7.00 C 2494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 483 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 141.8 milliseconds 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 892 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 13 through 36 removed outlier: 3.765A pdb=" N TYR A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 19 " --> pdb=" O TRP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.647A pdb=" N ALA A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 84 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 88 through 104 removed outlier: 3.835A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 126 through 161 Proline residue: A 152 - end of helix removed outlier: 3.511A pdb=" N GLY A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 180 Processing helix chain 'A' and resid 191 through 213 Processing helix chain 'A' and resid 215 through 226 removed outlier: 3.502A pdb=" N HIS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 4.197A pdb=" N THR A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 271 Processing helix chain 'A' and resid 275 through 307 removed outlier: 3.603A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.546A pdb=" N GLY A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 338 through 370 removed outlier: 4.119A pdb=" N THR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 409 removed outlier: 3.543A pdb=" N VAL A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 437 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 441 through 466 removed outlier: 3.740A pdb=" N THR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 546 removed outlier: 4.345A pdb=" N ALA A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 846 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: 0.52 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 638 1.33 - 1.45: 1013 1.45 - 1.57: 2172 1.57 - 1.70: 2 1.70 - 1.82: 42 Bond restraints: 3867 Sorted by residual: bond pdb=" O13 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.522 1.654 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" O11 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.703 1.644 0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" O12 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" O14 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.527 1.493 0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" C1 3PH A 704 " pdb=" O11 3PH A 704 " ideal model delta sigma weight residual 1.385 1.410 -0.025 2.00e-02 2.50e+03 1.50e+00 ... (remaining 3862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 5197 2.01 - 4.01: 64 4.01 - 6.02: 9 6.02 - 8.03: 0 8.03 - 10.04: 2 Bond angle restraints: 5272 Sorted by residual: angle pdb=" O12 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O14 3PH A 704 " ideal model delta sigma weight residual 113.84 123.88 -10.04 3.00e+00 1.11e-01 1.12e+01 angle pdb=" O13 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O14 3PH A 704 " ideal model delta sigma weight residual 115.01 104.99 10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA PRO A 512 " pdb=" C PRO A 512 " pdb=" N ALA A 513 " ideal model delta sigma weight residual 114.74 117.04 -2.30 1.03e+00 9.43e-01 4.97e+00 angle pdb=" O12 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O13 3PH A 704 " ideal model delta sigma weight residual 115.12 109.29 5.83 3.00e+00 1.11e-01 3.78e+00 angle pdb=" O11 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O14 3PH A 704 " ideal model delta sigma weight residual 104.78 110.05 -5.27 3.00e+00 1.11e-01 3.08e+00 ... (remaining 5267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 2015 15.89 - 31.78: 168 31.78 - 47.66: 32 47.66 - 63.55: 15 63.55 - 79.44: 2 Dihedral angle restraints: 2232 sinusoidal: 820 harmonic: 1412 Sorted by residual: dihedral pdb=" CA ASP A 309 " pdb=" C ASP A 309 " pdb=" N CYS A 310 " pdb=" CA CYS A 310 " ideal model delta harmonic sigma weight residual 180.00 -164.24 -15.76 0 5.00e+00 4.00e-02 9.93e+00 dihedral pdb=" CA HIS A 273 " pdb=" C HIS A 273 " pdb=" N THR A 274 " pdb=" CA THR A 274 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" CA LEU A 436 " pdb=" CB LEU A 436 " pdb=" CG LEU A 436 " pdb=" CD1 LEU A 436 " ideal model delta sinusoidal sigma weight residual 60.00 117.14 -57.14 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 471 0.039 - 0.079: 137 0.079 - 0.118: 24 0.118 - 0.158: 1 0.158 - 0.197: 1 Chirality restraints: 634 Sorted by residual: chirality pdb=" C2 3PH A 704 " pdb=" C1 3PH A 704 " pdb=" C3 3PH A 704 " pdb=" O21 3PH A 704 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA ILE A 229 " pdb=" N ILE A 229 " pdb=" C ILE A 229 " pdb=" CB ILE A 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA PRO A 337 " pdb=" N PRO A 337 " pdb=" C PRO A 337 " pdb=" CB PRO A 337 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 631 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 57 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO A 58 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 372 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO A 373 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 247 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C PHE A 247 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE A 247 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 248 " 0.009 2.00e-02 2.50e+03 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.72: 191 2.72 - 3.28: 4322 3.28 - 3.84: 6823 3.84 - 4.40: 8257 4.40 - 4.96: 14074 Nonbonded interactions: 33667 Sorted by model distance: nonbonded pdb=" O PHE A 125 " pdb=" OG SER A 126 " model vdw 2.160 3.040 nonbonded pdb=" OE1 GLN A 72 " pdb="NA NA A 702 " model vdw 2.201 2.470 nonbonded pdb=" OH TYR A 17 " pdb=" O THR A 160 " model vdw 2.261 3.040 nonbonded pdb=" O GLN A 414 " pdb=" OG1 THR A 418 " model vdw 2.338 3.040 nonbonded pdb=" O THR A 115 " pdb=" NE2 GLN A 267 " model vdw 2.343 3.120 ... (remaining 33662 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.550 Find NCS groups from input model: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 0.132 3868 Z= 0.226 Angle : 0.611 10.036 5274 Z= 0.307 Chirality : 0.037 0.197 634 Planarity : 0.005 0.055 639 Dihedral : 13.067 79.437 1337 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.51 % Allowed : 8.86 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.40), residues: 493 helix: 0.93 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -2.40 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 381 TYR 0.008 0.001 TYR A 348 PHE 0.009 0.001 PHE A 304 TRP 0.012 0.001 TRP A 165 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 ( 3867) covalent geometry : angle 0.61082 / 0.31 ( 5272) SS BOND : bond 0.00173 / 0.09 ( 1) SS BOND : angle 1.33499 / 0.89 ( 2) hydrogen bonds : bond 0.13769 / 8.20 ( 283) hydrogen bonds : angle 6.48125 / 4.76 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.130 Fit side-chains REVERT: A 154 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8196 (mt) REVERT: A 232 MET cc_start: 0.7860 (mmt) cc_final: 0.7589 (mmm) REVERT: A 269 TYR cc_start: 0.6460 (m-10) cc_final: 0.6194 (m-10) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.0636 time to fit residues: 5.2066 Evaluate side-chains 57 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN A 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.159555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140013 restraints weight = 3209.937| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.15 r_work: 0.3543 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3868 Z= 0.199 Angle : 0.635 9.089 5274 Z= 0.318 Chirality : 0.040 0.142 634 Planarity : 0.005 0.058 639 Dihedral : 8.370 59.958 567 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.78 % Allowed : 11.65 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.41), residues: 493 helix: 1.41 (0.28), residues: 383 sheet: None (None), residues: 0 loop : -2.06 (0.66), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 268 TYR 0.014 0.002 TYR A 118 PHE 0.014 0.002 PHE A 12 TRP 0.014 0.002 TRP A 165 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 3867) covalent geometry : angle 0.63452 / 0.32 ( 5272) SS BOND : bond 0.00548 / 0.29 ( 1) SS BOND : angle 1.34952 / 0.90 ( 2) hydrogen bonds : bond 0.04161 / 2.72 ( 283) hydrogen bonds : angle 4.71183 / 3.48 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: A 68 MET cc_start: 0.6822 (tmt) cc_final: 0.6478 (tmm) REVERT: A 154 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8080 (tt) REVERT: A 269 TYR cc_start: 0.6377 (m-10) cc_final: 0.6127 (m-10) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 0.0662 time to fit residues: 5.9708 Evaluate side-chains 63 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133470 restraints weight = 3204.843| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.17 r_work: 0.3561 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3868 Z= 0.153 Angle : 0.579 8.883 5274 Z= 0.294 Chirality : 0.039 0.145 634 Planarity : 0.005 0.057 639 Dihedral : 7.872 57.170 567 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.78 % Allowed : 13.67 % Favored : 83.54 % 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: 1.27 (0.41), residues: 493 helix: 1.60 (0.28), residues: 386 sheet: None (None), residues: 0 loop : -2.01 (0.66), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.012 0.001 TYR A 118 PHE 0.019 0.002 PHE A 12 TRP 0.013 0.001 TRP A 165 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 3867) covalent geometry : angle 0.57900 / 0.29 ( 5272) SS BOND : bond 0.00248 / 0.13 ( 1) SS BOND : angle 1.17110 / 0.78 ( 2) hydrogen bonds : bond 0.03684 / 2.42 ( 283) hydrogen bonds : angle 4.35075 / 3.22 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.142 Fit side-chains REVERT: A 154 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8191 (tt) REVERT: A 232 MET cc_start: 0.7989 (mmt) cc_final: 0.7630 (mmm) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.0644 time to fit residues: 5.5601 Evaluate side-chains 61 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** 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 = 0.3786 r_free = 0.3786 target = 0.154369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133910 restraints weight = 3209.929| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.20 r_work: 0.3474 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3868 Z= 0.149 Angle : 0.567 8.601 5274 Z= 0.285 Chirality : 0.039 0.172 634 Planarity : 0.005 0.058 639 Dihedral : 7.526 58.366 567 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.05 % Allowed : 13.16 % Favored : 82.78 % 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: 1.35 (0.41), residues: 493 helix: 1.62 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.82 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 268 TYR 0.010 0.001 TYR A 120 PHE 0.014 0.002 PHE A 304 TRP 0.013 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 3867) covalent geometry : angle 0.56688 / 0.29 ( 5272) SS BOND : bond 0.00212 / 0.11 ( 1) SS BOND : angle 0.98831 / 0.66 ( 2) hydrogen bonds : bond 0.03486 / 2.32 ( 283) hydrogen bonds : angle 4.20823 / 3.11 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.133 Fit side-chains REVERT: A 154 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8127 (tt) REVERT: A 206 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7194 (tp) outliers start: 16 outliers final: 9 residues processed: 74 average time/residue: 0.0650 time to fit residues: 6.1623 Evaluate side-chains 67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.153891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132812 restraints weight = 3338.333| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.25 r_work: 0.3460 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3868 Z= 0.163 Angle : 0.585 8.656 5274 Z= 0.292 Chirality : 0.039 0.144 634 Planarity : 0.005 0.059 639 Dihedral : 7.375 59.007 567 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.54 % Allowed : 15.19 % 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: 1.29 (0.41), residues: 493 helix: 1.58 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.85 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 268 TYR 0.010 0.001 TYR A 120 PHE 0.018 0.002 PHE A 12 TRP 0.013 0.001 TRP A 165 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 3867) covalent geometry : angle 0.58437 / 0.29 ( 5272) SS BOND : bond 0.00039 / 0.02 ( 1) SS BOND : angle 1.04098 / 0.69 ( 2) hydrogen bonds : bond 0.03478 / 2.30 ( 283) hydrogen bonds : angle 4.17638 / 3.09 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.142 Fit side-chains REVERT: A 15 TRP cc_start: 0.6396 (m-90) cc_final: 0.5656 (m100) REVERT: A 206 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7216 (tp) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.0677 time to fit residues: 5.9796 Evaluate side-chains 69 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 0.0570 chunk 40 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.155411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134094 restraints weight = 3444.723| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.28 r_work: 0.3473 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3868 Z= 0.141 Angle : 0.571 8.761 5274 Z= 0.285 Chirality : 0.038 0.143 634 Planarity : 0.005 0.058 639 Dihedral : 6.859 59.853 565 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.54 % Allowed : 15.95 % Favored : 80.51 % 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: 1.50 (0.41), residues: 493 helix: 1.71 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.73 (0.67), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.009 0.001 TYR A 120 PHE 0.014 0.002 PHE A 304 TRP 0.012 0.001 TRP A 165 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 3867) covalent geometry : angle 0.57133 / 0.29 ( 5272) SS BOND : bond 0.00357 / 0.19 ( 1) SS BOND : angle 0.76904 / 0.51 ( 2) hydrogen bonds : bond 0.03289 / 2.18 ( 283) hydrogen bonds : angle 4.05515 / 3.00 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.128 Fit side-chains REVERT: A 15 TRP cc_start: 0.6388 (m-90) cc_final: 0.5625 (m100) REVERT: A 206 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7143 (tp) REVERT: A 268 ARG cc_start: 0.7662 (mtt90) cc_final: 0.7129 (mpp80) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.0606 time to fit residues: 5.2770 Evaluate side-chains 70 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 0.0670 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.155406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134396 restraints weight = 3390.736| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.24 r_work: 0.3553 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3868 Z= 0.151 Angle : 0.591 11.461 5274 Z= 0.293 Chirality : 0.038 0.144 634 Planarity : 0.005 0.058 639 Dihedral : 6.717 58.538 565 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.05 % Allowed : 15.70 % Favored : 80.25 % 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: 1.48 (0.41), residues: 493 helix: 1.67 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.62 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.010 0.001 TYR A 269 PHE 0.014 0.002 PHE A 304 TRP 0.012 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 3867) covalent geometry : angle 0.59102 / 0.29 ( 5272) SS BOND : bond 0.00287 / 0.15 ( 1) SS BOND : angle 0.91697 / 0.61 ( 2) hydrogen bonds : bond 0.03325 / 2.20 ( 283) hydrogen bonds : angle 4.08259 / 3.03 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.135 Fit side-chains REVERT: A 15 TRP cc_start: 0.6411 (m-90) cc_final: 0.5668 (m100) REVERT: A 268 ARG cc_start: 0.7746 (mtt90) cc_final: 0.7266 (mpp80) outliers start: 16 outliers final: 12 residues processed: 70 average time/residue: 0.0623 time to fit residues: 5.6031 Evaluate side-chains 68 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 12 optimal weight: 0.2980 chunk 35 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.157633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136449 restraints weight = 3493.014| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.30 r_work: 0.3520 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3868 Z= 0.122 Angle : 0.560 10.802 5274 Z= 0.279 Chirality : 0.037 0.159 634 Planarity : 0.005 0.057 639 Dihedral : 6.469 58.806 565 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.04 % Allowed : 16.96 % Favored : 80.00 % 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 (0.41), residues: 493 helix: 1.84 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.59 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.011 0.001 TYR A 269 PHE 0.019 0.002 PHE A 12 TRP 0.011 0.001 TRP A 165 HIS 0.001 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 3867) covalent geometry : angle 0.56050 / 0.28 ( 5272) SS BOND : bond 0.00227 / 0.12 ( 1) SS BOND : angle 0.52533 / 0.35 ( 2) hydrogen bonds : bond 0.03105 / 2.08 ( 283) hydrogen bonds : angle 3.93943 / 2.92 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.152 Fit side-chains REVERT: A 15 TRP cc_start: 0.6338 (m-90) cc_final: 0.5504 (m100) REVERT: A 268 ARG cc_start: 0.7692 (mtt90) cc_final: 0.7194 (mpp80) outliers start: 12 outliers final: 10 residues processed: 70 average time/residue: 0.0713 time to fit residues: 6.2637 Evaluate side-chains 67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 13 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 = 0.3846 r_free = 0.3846 target = 0.159564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139375 restraints weight = 3337.879| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.20 r_work: 0.3556 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3868 Z= 0.157 Angle : 0.604 13.550 5274 Z= 0.297 Chirality : 0.039 0.162 634 Planarity : 0.005 0.058 639 Dihedral : 6.406 59.275 565 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.04 % Allowed : 17.97 % Favored : 78.99 % 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: 1.54 (0.41), residues: 493 helix: 1.71 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.62 (0.66), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.011 0.001 TYR A 348 PHE 0.017 0.002 PHE A 12 TRP 0.011 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 3867) covalent geometry : angle 0.60419 / 0.30 ( 5272) SS BOND : bond 0.00246 / 0.13 ( 1) SS BOND : angle 0.76852 / 0.51 ( 2) hydrogen bonds : bond 0.03305 / 2.18 ( 283) hydrogen bonds : angle 4.09056 / 3.02 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.132 Fit side-chains REVERT: A 15 TRP cc_start: 0.6415 (m-90) cc_final: 0.5600 (m100) REVERT: A 268 ARG cc_start: 0.7727 (mtt90) cc_final: 0.7265 (mpp80) outliers start: 12 outliers final: 11 residues processed: 66 average time/residue: 0.0680 time to fit residues: 5.7273 Evaluate side-chains 67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 16 optimal weight: 0.0470 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.0770 overall best weight: 0.3034 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.159021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137661 restraints weight = 3449.320| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.28 r_work: 0.3544 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3868 Z= 0.119 Angle : 0.574 14.823 5274 Z= 0.281 Chirality : 0.037 0.161 634 Planarity : 0.005 0.057 639 Dihedral : 6.138 59.790 565 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.78 % Allowed : 18.73 % Favored : 78.48 % 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: 493 helix: 1.90 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.59 (0.66), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.010 0.001 TYR A 348 PHE 0.022 0.002 PHE A 518 TRP 0.011 0.001 TRP A 165 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 3867) covalent geometry : angle 0.57372 / 0.28 ( 5272) SS BOND : bond 0.00185 / 0.10 ( 1) SS BOND : angle 0.42871 / 0.29 ( 2) hydrogen bonds : bond 0.03019 / 2.01 ( 283) hydrogen bonds : angle 3.94601 / 2.92 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.136 Fit side-chains REVERT: A 15 TRP cc_start: 0.6293 (m-90) cc_final: 0.5468 (m100) REVERT: A 82 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7500 (mtp85) REVERT: A 268 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7268 (mpp80) outliers start: 11 outliers final: 10 residues processed: 69 average time/residue: 0.0703 time to fit residues: 6.1067 Evaluate side-chains 70 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.158322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136735 restraints weight = 3454.727| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.29 r_work: 0.3518 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3868 Z= 0.130 Angle : 0.582 14.631 5274 Z= 0.287 Chirality : 0.037 0.162 634 Planarity : 0.004 0.056 639 Dihedral : 5.999 59.361 565 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.78 % Allowed : 19.24 % Favored : 77.97 % 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: 1.80 (0.41), residues: 493 helix: 1.91 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -1.60 (0.66), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.010 0.001 TYR A 348 PHE 0.016 0.001 PHE A 12 TRP 0.010 0.001 TRP A 165 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 3867) covalent geometry : angle 0.58212 / 0.29 ( 5272) SS BOND : bond 0.00223 / 0.12 ( 1) SS BOND : angle 0.52902 / 0.35 ( 2) hydrogen bonds : bond 0.03076 / 2.05 ( 283) hydrogen bonds : angle 3.94859 / 2.92 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1222.33 seconds wall clock time: 21 minutes 37.98 seconds (1297.98 seconds total)