Starting phenix.real_space_refine on Tue Aug 4 15:36:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wbr_65847/08_2026/9wbr_65847.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wbr_65847/08_2026/9wbr_65847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wbr_65847/08_2026/9wbr_65847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wbr_65847/08_2026/9wbr_65847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wbr_65847/08_2026/9wbr_65847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wbr_65847/08_2026/9wbr_65847.map" } resolution = 3.13 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= -0.003 sd= 0.106 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 S 34 5.16 5 Cl 1 4.86 5 C 2931 2.51 5 N 667 2.21 5 O 735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4368 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4367 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 31, 'TRANS': 525} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.92, per 1000 atoms: 0.21 Number of scatterers: 4368 At special positions: 0 Unit cell: (81.092, 66.154, 91.762, 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) Cl 1 17.00 S 34 16.00 O 735 8.00 N 667 7.00 C 2931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 320 " 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: 0.22 Conformation dependent library (CDL) restraints added in 96.7 milliseconds 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 76.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 197 through 207 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 215 through 225 Processing helix chain 'A' and resid 226 through 241 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 241 through 256 removed outlier: 3.850A pdb=" N ALA A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 265 removed outlier: 3.616A pdb=" N TRP A 263 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 300 removed outlier: 3.654A pdb=" N GLY A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 393 through 414 Processing helix chain 'A' and resid 423 through 442 Proline residue: A 429 - end of helix removed outlier: 3.851A pdb=" N THR A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 455 removed outlier: 3.809A pdb=" N GLY A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 463 through 478 removed outlier: 3.711A pdb=" N TRP A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 removed outlier: 3.600A pdb=" N THR A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 532 Processing helix chain 'A' and resid 544 through 555 Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 559 through 594 removed outlier: 3.537A pdb=" N TRP A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 removed outlier: 4.438A pdb=" N THR A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 617 Processing helix chain 'A' and resid 618 through 621 Processing helix chain 'A' and resid 624 through 636 Processing helix chain 'A' and resid 638 through 654 Processing helix chain 'A' and resid 657 through 670 Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 683 through 699 Processing helix chain 'A' and resid 711 through 727 removed outlier: 3.734A pdb=" N SER A 725 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 743 through 753 Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.687A pdb=" N ARG A 766 " --> pdb=" O ALA A 763 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 861 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: 0.54 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1265 1.34 - 1.46: 1050 1.46 - 1.58: 2140 1.58 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 4507 Sorted by residual: bond pdb=" C ASN A 537 " pdb=" N VAL A 538 " ideal model delta sigma weight residual 1.335 1.291 0.044 1.21e-02 6.83e+03 1.35e+01 bond pdb=" N VAL A 684 " pdb=" CA VAL A 684 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.10e+01 bond pdb=" N ILE A 669 " pdb=" CA ILE A 669 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N ILE A 415 " pdb=" CA ILE A 415 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.00e+01 bond pdb=" C VAL A 538 " pdb=" N ALA A 539 " ideal model delta sigma weight residual 1.331 1.369 -0.039 1.23e-02 6.61e+03 9.95e+00 ... (remaining 4502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 5888 1.88 - 3.76: 238 3.76 - 5.63: 26 5.63 - 7.51: 2 7.51 - 9.39: 1 Bond angle restraints: 6155 Sorted by residual: angle pdb=" C LEU A 198 " pdb=" N ASP A 199 " pdb=" CA ASP A 199 " ideal model delta sigma weight residual 120.54 115.63 4.91 1.35e+00 5.49e-01 1.33e+01 angle pdb=" CA CYS A 331 " pdb=" C CYS A 331 " pdb=" O CYS A 331 " ideal model delta sigma weight residual 121.33 117.62 3.71 1.08e+00 8.57e-01 1.18e+01 angle pdb=" O VAL A 538 " pdb=" C VAL A 538 " pdb=" N ALA A 539 " ideal model delta sigma weight residual 121.87 125.26 -3.39 1.01e+00 9.80e-01 1.13e+01 angle pdb=" CA THR A 427 " pdb=" CB THR A 427 " pdb=" OG1 THR A 427 " ideal model delta sigma weight residual 109.60 104.73 4.87 1.50e+00 4.44e-01 1.06e+01 angle pdb=" CA ILE A 201 " pdb=" C ILE A 201 " pdb=" O ILE A 201 " ideal model delta sigma weight residual 121.05 117.53 3.52 1.11e+00 8.12e-01 1.00e+01 ... (remaining 6150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 2280 16.76 - 33.52: 215 33.52 - 50.27: 58 50.27 - 67.03: 12 67.03 - 83.79: 2 Dihedral angle restraints: 2567 sinusoidal: 954 harmonic: 1613 Sorted by residual: dihedral pdb=" CA TRP A 315 " pdb=" C TRP A 315 " pdb=" N ASN A 316 " pdb=" CA ASN A 316 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CB CYS A 311 " pdb=" SG CYS A 311 " pdb=" SG CYS A 320 " pdb=" CB CYS A 320 " ideal model delta sinusoidal sigma weight residual -86.00 -116.58 30.58 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CA TRP A 263 " pdb=" C TRP A 263 " pdb=" N LYS A 264 " pdb=" CA LYS A 264 " ideal model delta harmonic sigma weight residual 180.00 164.00 16.00 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 2564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 473 0.046 - 0.093: 150 0.093 - 0.139: 62 0.139 - 0.185: 9 0.185 - 0.232: 2 Chirality restraints: 696 Sorted by residual: chirality pdb=" CA VAL A 422 " pdb=" N VAL A 422 " pdb=" C VAL A 422 " pdb=" CB VAL A 422 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL A 332 " pdb=" N VAL A 332 " pdb=" C VAL A 332 " pdb=" CB VAL A 332 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA ILE A 665 " pdb=" N ILE A 665 " pdb=" C ILE A 665 " pdb=" CB ILE A 665 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 693 not shown) Planarity restraints: 749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 623 " 0.013 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C GLN A 623 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN A 623 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY A 624 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 283 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ILE A 283 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE A 283 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 284 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 284 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C ALA A 284 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA A 284 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 285 " 0.011 2.00e-02 2.50e+03 ... (remaining 746 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 2190 2.96 - 3.45: 4787 3.45 - 3.93: 7337 3.93 - 4.42: 8585 4.42 - 4.90: 13779 Nonbonded interactions: 36678 Sorted by model distance: nonbonded pdb=" OH TYR A 233 " pdb="CL CL A 801 " model vdw 2.481 3.190 nonbonded pdb=" OG SER A 513 " pdb="CL CL A 801 " model vdw 2.497 3.190 nonbonded pdb=" O LYS A 197 " pdb=" N ASP A 199 " model vdw 2.513 3.120 nonbonded pdb=" O TYR A 423 " pdb=" N ALA A 426 " model vdw 2.522 3.120 nonbonded pdb=" O LYS A 197 " pdb=" C LEU A 198 " model vdw 2.531 3.270 ... (remaining 36673 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: 1.960 Set stop_for_unknowns flag: 0.010 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.610 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.006 0.044 4508 Z= 0.406 Angle : 0.761 9.389 6157 Z= 0.508 Chirality : 0.053 0.232 696 Planarity : 0.005 0.029 749 Dihedral : 14.297 83.790 1532 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % 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: 0.86 (0.34), residues: 551 helix: 1.01 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.18 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.021 0.001 TYR A 286 PHE 0.019 0.001 PHE A 401 TRP 0.012 0.001 TRP A 404 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.41 ( 4507) covalent geometry : angle 0.76063 / 0.51 ( 6155) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 1.27803 / 0.69 ( 2) hydrogen bonds : bond 0.14095 / 9.68 ( 291) hydrogen bonds : angle 7.35066 / 5.40 ( 861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.097 Fit side-chains REVERT: A 303 VAL cc_start: 0.7990 (p) cc_final: 0.7656 (m) REVERT: A 319 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7752 (tt0) REVERT: A 373 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8221 (mm-30) REVERT: A 436 LEU cc_start: 0.8476 (mt) cc_final: 0.8211 (mt) REVERT: A 499 TYR cc_start: 0.8640 (t80) cc_final: 0.8055 (t80) REVERT: A 666 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7748 (tt0) REVERT: A 749 LYS cc_start: 0.8403 (ttpp) cc_final: 0.7509 (mttm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0531 time to fit residues: 8.5647 Evaluate side-chains 89 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN A 601 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.128018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.106960 restraints weight = 5661.435| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.76 r_work: 0.3105 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4508 Z= 0.169 Angle : 0.591 7.235 6157 Z= 0.301 Chirality : 0.042 0.131 696 Planarity : 0.005 0.041 749 Dihedral : 4.066 17.582 593 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.82 % Allowed : 15.40 % Favored : 81.78 % 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: 2.13 (0.35), residues: 551 helix: 1.93 (0.26), residues: 378 sheet: None (None), residues: 0 loop : 0.36 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 556 TYR 0.021 0.002 TYR A 286 PHE 0.016 0.001 PHE A 683 TRP 0.009 0.001 TRP A 482 HIS 0.001 0.000 HIS A 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 4507) covalent geometry : angle 0.59105 / 0.30 ( 6155) SS BOND : bond 0.00124 / 0.07 ( 1) SS BOND : angle 1.15526 / 0.61 ( 2) hydrogen bonds : bond 0.05144 / 3.47 ( 291) hydrogen bonds : angle 4.93096 / 3.63 ( 861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.159 Fit side-chains REVERT: A 235 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: A 277 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8265 (mp) REVERT: A 436 LEU cc_start: 0.8577 (mt) cc_final: 0.8330 (mt) REVERT: A 499 TYR cc_start: 0.8497 (t80) cc_final: 0.7990 (t80) REVERT: A 727 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7745 (pt) REVERT: A 749 LYS cc_start: 0.8473 (ttpp) cc_final: 0.7628 (mttm) outliers start: 13 outliers final: 7 residues processed: 99 average time/residue: 0.0462 time to fit residues: 6.1816 Evaluate side-chains 88 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 0.0040 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 0.0000 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.125902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.104223 restraints weight = 5602.807| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.82 r_work: 0.3052 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4508 Z= 0.144 Angle : 0.552 7.235 6157 Z= 0.279 Chirality : 0.041 0.138 696 Planarity : 0.005 0.046 749 Dihedral : 4.067 17.186 593 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.25 % Allowed : 14.53 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.36), residues: 551 helix: 2.15 (0.26), residues: 373 sheet: None (None), residues: 0 loop : 0.28 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 556 TYR 0.023 0.001 TYR A 286 PHE 0.019 0.001 PHE A 683 TRP 0.011 0.001 TRP A 482 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 4507) covalent geometry : angle 0.55127 / 0.28 ( 6155) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 1.11085 / 0.60 ( 2) hydrogen bonds : bond 0.04564 / 3.06 ( 291) hydrogen bonds : angle 4.64032 / 3.44 ( 861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.096 Fit side-chains REVERT: A 235 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8213 (mtm) REVERT: A 277 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8290 (mp) REVERT: A 436 LEU cc_start: 0.8515 (mt) cc_final: 0.8243 (mt) REVERT: A 463 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7743 (t70) REVERT: A 499 TYR cc_start: 0.8588 (t80) cc_final: 0.8075 (t80) REVERT: A 633 ASP cc_start: 0.9050 (t0) cc_final: 0.8676 (t0) REVERT: A 727 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7742 (pt) REVERT: A 746 GLU cc_start: 0.8035 (mp0) cc_final: 0.7399 (tp30) REVERT: A 749 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7435 (mttm) outliers start: 15 outliers final: 7 residues processed: 101 average time/residue: 0.0415 time to fit residues: 5.7432 Evaluate side-chains 92 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.106395 restraints weight = 5473.542| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.61 r_work: 0.3007 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4508 Z= 0.173 Angle : 0.565 7.756 6157 Z= 0.286 Chirality : 0.042 0.141 696 Planarity : 0.005 0.045 749 Dihedral : 4.205 19.271 593 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.90 % Allowed : 14.75 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.35), residues: 551 helix: 2.09 (0.25), residues: 377 sheet: None (None), residues: 0 loop : 0.26 (0.51), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.024 0.002 TYR A 286 PHE 0.015 0.001 PHE A 683 TRP 0.012 0.001 TRP A 482 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 ( 4507) covalent geometry : angle 0.56487 / 0.29 ( 6155) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 1.07249 / 0.59 ( 2) hydrogen bonds : bond 0.04652 / 3.09 ( 291) hydrogen bonds : angle 4.67421 / 3.46 ( 861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.099 Fit side-chains REVERT: A 235 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8204 (mtm) REVERT: A 277 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 302 PHE cc_start: 0.6686 (m-10) cc_final: 0.6050 (m-80) REVERT: A 322 ASP cc_start: 0.7208 (p0) cc_final: 0.6967 (p0) REVERT: A 436 LEU cc_start: 0.8541 (mt) cc_final: 0.8282 (mt) REVERT: A 499 TYR cc_start: 0.8577 (t80) cc_final: 0.8050 (t80) REVERT: A 501 ASP cc_start: 0.8401 (m-30) cc_final: 0.8153 (m-30) REVERT: A 633 ASP cc_start: 0.9157 (t0) cc_final: 0.8824 (t0) REVERT: A 683 PHE cc_start: 0.8477 (t80) cc_final: 0.8224 (t80) REVERT: A 727 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7728 (pt) REVERT: A 749 LYS cc_start: 0.8279 (ttpp) cc_final: 0.7380 (mttm) outliers start: 18 outliers final: 11 residues processed: 89 average time/residue: 0.0303 time to fit residues: 3.9242 Evaluate side-chains 87 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 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 = 0.3335 r_free = 0.3335 target = 0.123756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.103104 restraints weight = 5585.326| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.70 r_work: 0.2992 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4508 Z= 0.142 Angle : 0.546 8.311 6157 Z= 0.274 Chirality : 0.041 0.141 696 Planarity : 0.004 0.043 749 Dihedral : 4.135 18.734 593 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.47 % Allowed : 15.18 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.36), residues: 551 helix: 2.17 (0.25), residues: 377 sheet: None (None), residues: 0 loop : 0.29 (0.50), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 747 TYR 0.022 0.001 TYR A 286 PHE 0.010 0.001 PHE A 683 TRP 0.012 0.001 TRP A 482 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 4507) covalent geometry : angle 0.54552 / 0.27 ( 6155) SS BOND : bond 0.00062 / 0.03 ( 1) SS BOND : angle 1.24524 / 0.68 ( 2) hydrogen bonds : bond 0.04458 / 2.95 ( 291) hydrogen bonds : angle 4.62492 / 3.43 ( 861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.110 Fit side-chains REVERT: A 235 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8226 (mtm) REVERT: A 277 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 302 PHE cc_start: 0.6796 (m-10) cc_final: 0.6122 (m-80) REVERT: A 322 ASP cc_start: 0.7164 (p0) cc_final: 0.6917 (p0) REVERT: A 436 LEU cc_start: 0.8532 (mt) cc_final: 0.8279 (mt) REVERT: A 499 TYR cc_start: 0.8586 (t80) cc_final: 0.8068 (t80) REVERT: A 501 ASP cc_start: 0.8526 (m-30) cc_final: 0.8251 (m-30) REVERT: A 633 ASP cc_start: 0.9146 (t70) cc_final: 0.8822 (t0) REVERT: A 644 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.9000 (mt) REVERT: A 683 PHE cc_start: 0.8488 (t80) cc_final: 0.8207 (t80) REVERT: A 727 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7771 (pt) REVERT: A 749 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7391 (mttm) REVERT: A 773 MET cc_start: 0.8405 (ptm) cc_final: 0.8136 (ptm) outliers start: 16 outliers final: 7 residues processed: 90 average time/residue: 0.0423 time to fit residues: 5.2595 Evaluate side-chains 88 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 765 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111406 restraints weight = 5383.553| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.61 r_work: 0.3137 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4508 Z= 0.143 Angle : 0.543 8.673 6157 Z= 0.272 Chirality : 0.041 0.145 696 Planarity : 0.004 0.041 749 Dihedral : 4.096 18.608 593 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.69 % Allowed : 15.18 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.35), residues: 551 helix: 2.19 (0.25), residues: 377 sheet: None (None), residues: 0 loop : 0.28 (0.50), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 556 TYR 0.024 0.001 TYR A 286 PHE 0.011 0.001 PHE A 515 TRP 0.012 0.001 TRP A 482 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 4507) covalent geometry : angle 0.54274 / 0.27 ( 6155) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 1.22348 / 0.67 ( 2) hydrogen bonds : bond 0.04367 / 2.88 ( 291) hydrogen bonds : angle 4.57808 / 3.39 ( 861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.160 Fit side-chains REVERT: A 235 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: A 277 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8324 (mp) REVERT: A 302 PHE cc_start: 0.7233 (m-10) cc_final: 0.6816 (m-80) REVERT: A 322 ASP cc_start: 0.7151 (p0) cc_final: 0.6928 (p0) REVERT: A 373 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: A 436 LEU cc_start: 0.8478 (mt) cc_final: 0.8231 (mt) REVERT: A 461 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7875 (mp) REVERT: A 499 TYR cc_start: 0.8605 (t80) cc_final: 0.8025 (t80) REVERT: A 501 ASP cc_start: 0.8576 (m-30) cc_final: 0.8302 (m-30) REVERT: A 633 ASP cc_start: 0.9206 (t70) cc_final: 0.8913 (t0) REVERT: A 683 PHE cc_start: 0.8440 (t80) cc_final: 0.8135 (t80) REVERT: A 727 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7646 (pt) REVERT: A 749 LYS cc_start: 0.8032 (ttpp) cc_final: 0.7057 (mttm) REVERT: A 773 MET cc_start: 0.8366 (ptm) cc_final: 0.8043 (ptm) outliers start: 17 outliers final: 10 residues processed: 89 average time/residue: 0.0324 time to fit residues: 4.0780 Evaluate side-chains 89 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 33 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.131849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112742 restraints weight = 5290.519| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.58 r_work: 0.3154 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4508 Z= 0.129 Angle : 0.531 9.183 6157 Z= 0.266 Chirality : 0.041 0.139 696 Planarity : 0.004 0.040 749 Dihedral : 4.027 18.290 593 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.56 % Allowed : 13.88 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.35), residues: 551 helix: 2.28 (0.25), residues: 377 sheet: None (None), residues: 0 loop : 0.32 (0.50), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 709 TYR 0.022 0.001 TYR A 286 PHE 0.008 0.001 PHE A 521 TRP 0.013 0.001 TRP A 263 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 4507) covalent geometry : angle 0.53067 / 0.27 ( 6155) SS BOND : bond 0.00019 / 0.01 ( 1) SS BOND : angle 1.00440 / 0.54 ( 2) hydrogen bonds : bond 0.04269 / 2.81 ( 291) hydrogen bonds : angle 4.53306 / 3.36 ( 861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.105 Fit side-chains REVERT: A 235 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8097 (mtm) REVERT: A 277 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 287 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: A 373 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: A 436 LEU cc_start: 0.8442 (mt) cc_final: 0.8198 (mt) REVERT: A 461 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 463 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7266 (t70) REVERT: A 499 TYR cc_start: 0.8630 (t80) cc_final: 0.8084 (t80) REVERT: A 501 ASP cc_start: 0.8550 (m-30) cc_final: 0.8307 (m-30) REVERT: A 579 MET cc_start: 0.8779 (mmm) cc_final: 0.8499 (mmm) REVERT: A 633 ASP cc_start: 0.9193 (t70) cc_final: 0.8892 (t0) REVERT: A 683 PHE cc_start: 0.8404 (t80) cc_final: 0.8101 (t80) REVERT: A 712 ASN cc_start: 0.7853 (m-40) cc_final: 0.7390 (t0) REVERT: A 727 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7605 (pt) REVERT: A 746 GLU cc_start: 0.8254 (mp0) cc_final: 0.8033 (mp0) REVERT: A 749 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7289 (mttm) REVERT: A 773 MET cc_start: 0.8362 (ptm) cc_final: 0.8027 (ptm) outliers start: 21 outliers final: 9 residues processed: 87 average time/residue: 0.0325 time to fit residues: 4.0892 Evaluate side-chains 89 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 0.0370 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.129908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110276 restraints weight = 5309.902| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.60 r_work: 0.3118 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4508 Z= 0.159 Angle : 0.553 9.585 6157 Z= 0.277 Chirality : 0.042 0.141 696 Planarity : 0.004 0.039 749 Dihedral : 4.085 18.396 593 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.47 % Allowed : 15.62 % Favored : 80.91 % 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: 2.44 (0.35), residues: 551 helix: 2.21 (0.25), residues: 377 sheet: None (None), residues: 0 loop : 0.36 (0.51), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.023 0.001 TYR A 286 PHE 0.013 0.001 PHE A 515 TRP 0.012 0.001 TRP A 482 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 4507) covalent geometry : angle 0.55309 / 0.28 ( 6155) SS BOND : bond 0.00345 / 0.18 ( 1) SS BOND : angle 1.28345 / 0.68 ( 2) hydrogen bonds : bond 0.04437 / 2.92 ( 291) hydrogen bonds : angle 4.59483 / 3.40 ( 861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.102 Fit side-chains REVERT: A 235 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8100 (mtm) REVERT: A 277 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 373 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: A 436 LEU cc_start: 0.8492 (mt) cc_final: 0.8264 (mt) REVERT: A 463 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7214 (t70) REVERT: A 499 TYR cc_start: 0.8622 (t80) cc_final: 0.8048 (t80) REVERT: A 501 ASP cc_start: 0.8582 (m-30) cc_final: 0.8331 (m-30) REVERT: A 579 MET cc_start: 0.8898 (mmm) cc_final: 0.8664 (mmm) REVERT: A 620 MET cc_start: 0.8852 (mtm) cc_final: 0.8519 (mtt) REVERT: A 633 ASP cc_start: 0.9244 (t70) cc_final: 0.8952 (t0) REVERT: A 683 PHE cc_start: 0.8432 (t80) cc_final: 0.8104 (t80) REVERT: A 712 ASN cc_start: 0.7902 (m-40) cc_final: 0.7457 (t0) REVERT: A 727 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7625 (pt) REVERT: A 749 LYS cc_start: 0.8060 (ttpp) cc_final: 0.7112 (mttm) REVERT: A 773 MET cc_start: 0.8424 (ptm) cc_final: 0.8076 (ptm) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.0478 time to fit residues: 5.7179 Evaluate side-chains 88 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 775 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 19 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.128778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109364 restraints weight = 5341.956| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.59 r_work: 0.3125 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4508 Z= 0.152 Angle : 0.560 9.549 6157 Z= 0.280 Chirality : 0.041 0.141 696 Planarity : 0.004 0.038 749 Dihedral : 4.063 18.268 593 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.25 % Allowed : 16.27 % Favored : 80.48 % 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: 2.44 (0.36), residues: 551 helix: 2.18 (0.25), residues: 377 sheet: None (None), residues: 0 loop : 0.44 (0.51), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.022 0.001 TYR A 286 PHE 0.010 0.001 PHE A 526 TRP 0.013 0.001 TRP A 482 HIS 0.001 0.000 HIS A 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 4507) covalent geometry : angle 0.55981 / 0.28 ( 6155) SS BOND : bond 0.00052 / 0.03 ( 1) SS BOND : angle 1.19386 / 0.65 ( 2) hydrogen bonds : bond 0.04390 / 2.90 ( 291) hydrogen bonds : angle 4.58525 / 3.40 ( 861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.097 Fit side-chains REVERT: A 235 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8079 (mtm) REVERT: A 277 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8299 (mp) REVERT: A 373 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: A 436 LEU cc_start: 0.8444 (mt) cc_final: 0.8237 (mt) REVERT: A 463 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7257 (t0) REVERT: A 499 TYR cc_start: 0.8616 (t80) cc_final: 0.8071 (t80) REVERT: A 501 ASP cc_start: 0.8598 (m-30) cc_final: 0.8387 (m-30) REVERT: A 620 MET cc_start: 0.8869 (mtm) cc_final: 0.8524 (mtt) REVERT: A 633 ASP cc_start: 0.9222 (t70) cc_final: 0.8945 (t0) REVERT: A 683 PHE cc_start: 0.8413 (t80) cc_final: 0.8087 (t80) REVERT: A 712 ASN cc_start: 0.7911 (m-40) cc_final: 0.7465 (t0) REVERT: A 727 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7621 (pt) REVERT: A 749 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7123 (mttm) REVERT: A 773 MET cc_start: 0.8427 (ptm) cc_final: 0.8076 (ptm) outliers start: 15 outliers final: 10 residues processed: 84 average time/residue: 0.0371 time to fit residues: 4.2980 Evaluate side-chains 87 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.130628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111253 restraints weight = 5293.886| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.59 r_work: 0.3135 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4508 Z= 0.140 Angle : 0.545 9.541 6157 Z= 0.271 Chirality : 0.041 0.141 696 Planarity : 0.004 0.035 749 Dihedral : 4.012 18.210 593 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.47 % Allowed : 16.05 % Favored : 80.48 % 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: 2.51 (0.36), residues: 551 helix: 2.24 (0.25), residues: 377 sheet: None (None), residues: 0 loop : 0.48 (0.51), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.023 0.001 TYR A 286 PHE 0.016 0.001 PHE A 515 TRP 0.013 0.001 TRP A 482 HIS 0.001 0.000 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 4507) covalent geometry : angle 0.54434 / 0.27 ( 6155) SS BOND : bond 0.00068 / 0.04 ( 1) SS BOND : angle 1.26500 / 0.69 ( 2) hydrogen bonds : bond 0.04341 / 2.86 ( 291) hydrogen bonds : angle 4.56542 / 3.38 ( 861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.146 Fit side-chains REVERT: A 235 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8026 (mtm) REVERT: A 277 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8290 (mp) REVERT: A 373 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: A 436 LEU cc_start: 0.8435 (mt) cc_final: 0.8228 (mt) REVERT: A 463 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7246 (t0) REVERT: A 499 TYR cc_start: 0.8623 (t80) cc_final: 0.8091 (t80) REVERT: A 501 ASP cc_start: 0.8647 (m-30) cc_final: 0.8412 (m-30) REVERT: A 633 ASP cc_start: 0.9203 (t70) cc_final: 0.8935 (t0) REVERT: A 683 PHE cc_start: 0.8418 (t80) cc_final: 0.8098 (t80) REVERT: A 712 ASN cc_start: 0.7922 (m-40) cc_final: 0.7477 (t0) REVERT: A 727 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7620 (pt) REVERT: A 749 LYS cc_start: 0.8017 (ttpp) cc_final: 0.7123 (mttm) REVERT: A 773 MET cc_start: 0.8408 (ptm) cc_final: 0.8058 (ptm) outliers start: 16 outliers final: 9 residues processed: 84 average time/residue: 0.0440 time to fit residues: 5.1340 Evaluate side-chains 86 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 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 = 0.3454 r_free = 0.3454 target = 0.129241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.109900 restraints weight = 5354.766| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.59 r_work: 0.3116 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4508 Z= 0.163 Angle : 0.572 9.698 6157 Z= 0.285 Chirality : 0.042 0.154 696 Planarity : 0.004 0.034 749 Dihedral : 4.062 18.541 593 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.47 % Allowed : 16.05 % Favored : 80.48 % 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: 2.44 (0.36), residues: 551 helix: 2.17 (0.25), residues: 377 sheet: None (None), residues: 0 loop : 0.48 (0.51), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.023 0.001 TYR A 286 PHE 0.010 0.001 PHE A 526 TRP 0.013 0.001 TRP A 263 HIS 0.001 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 4507) covalent geometry : angle 0.57186 / 0.29 ( 6155) SS BOND : bond 0.00016 / 0.01 ( 1) SS BOND : angle 1.31780 / 0.72 ( 2) hydrogen bonds : bond 0.04457 / 2.94 ( 291) hydrogen bonds : angle 4.60637 / 3.41 ( 861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 924.81 seconds wall clock time: 16 minutes 27.16 seconds (987.16 seconds total)