Starting phenix.real_space_refine on Thu Jul 2 00:50:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wmv_32617/07_2026/7wmv_32617.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wmv_32617/07_2026/7wmv_32617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wmv_32617/07_2026/7wmv_32617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wmv_32617/07_2026/7wmv_32617.map" model { file = "/net/cci-nas-00/data/ceres_data/7wmv_32617/07_2026/7wmv_32617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wmv_32617/07_2026/7wmv_32617.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.155 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 3252 2.51 5 N 776 2.21 5 O 830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 4899 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4608 Classifications: {'peptide': 602} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 22, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 254 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'1YI': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.21, per 1000 atoms: 0.25 Number of scatterers: 4899 At special positions: 0 Unit cell: (91.131, 73.89, 84.563, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 830 8.00 N 776 7.00 C 3252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.02 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: 0.44 Conformation dependent library (CDL) restraints added in 180.1 milliseconds 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 21 through 25 removed outlier: 3.838A pdb=" N ASN A 25 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 48 Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.690A pdb=" N ILE A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 99 through 124 removed outlier: 3.504A pdb=" N LEU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 107 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 138 through 173 removed outlier: 3.987A pdb=" N GLN A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 4.298A pdb=" N TYR A 191 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 226 removed outlier: 4.307A pdb=" N LEU A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.610A pdb=" N MET A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 291 removed outlier: 3.642A pdb=" N TRP A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.571A pdb=" N VAL A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 removed outlier: 4.111A pdb=" N VAL A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 355 removed outlier: 3.757A pdb=" N CYS A 355 " --> pdb=" O CYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.876A pdb=" N MET A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 408 removed outlier: 3.655A pdb=" N SER A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 418 through 447 removed outlier: 3.568A pdb=" N SER A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 451 through 476 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.888A pdb=" N TYR A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 525 through 548 Processing helix chain 'A' and resid 552 through 557 removed outlier: 4.204A pdb=" N TYR A 557 " --> pdb=" O VAL A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 633 Processing helix chain 'A' and resid 638 through 664 Processing helix chain 'B' and resid 28 through 54 removed outlier: 3.855A pdb=" N GLY B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1059 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: 0.80 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 726 1.31 - 1.44: 1394 1.44 - 1.57: 2833 1.57 - 1.70: 0 1.70 - 1.83: 67 Bond restraints: 5020 Sorted by residual: bond pdb=" C36 1YI A 701 " pdb=" N9 1YI A 701 " ideal model delta sigma weight residual 1.341 1.454 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" C35 1YI A 701 " pdb=" N8 1YI A 701 " ideal model delta sigma weight residual 1.351 1.455 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C GLN B 22 " pdb=" N GLY B 23 " ideal model delta sigma weight residual 1.331 1.352 -0.021 6.60e-03 2.30e+04 1.04e+01 bond pdb=" CA GLY B 23 " pdb=" C GLY B 23 " ideal model delta sigma weight residual 1.517 1.496 0.022 7.00e-03 2.04e+04 9.70e+00 bond pdb=" CA VAL A 117 " pdb=" CB VAL A 117 " ideal model delta sigma weight residual 1.534 1.515 0.020 6.80e-03 2.16e+04 8.40e+00 ... (remaining 5015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6377 1.71 - 3.43: 382 3.43 - 5.14: 58 5.14 - 6.85: 14 6.85 - 8.57: 8 Bond angle restraints: 6839 Sorted by residual: angle pdb=" N PRO A 324 " pdb=" CA PRO A 324 " pdb=" C PRO A 324 " ideal model delta sigma weight residual 112.47 120.07 -7.60 2.06e+00 2.36e-01 1.36e+01 angle pdb=" C ILE A 167 " pdb=" N PHE A 168 " pdb=" CA PHE A 168 " ideal model delta sigma weight residual 121.14 116.17 4.97 1.75e+00 3.27e-01 8.06e+00 angle pdb=" N GLY A 95 " pdb=" CA GLY A 95 " pdb=" C GLY A 95 " ideal model delta sigma weight residual 113.18 119.64 -6.46 2.37e+00 1.78e-01 7.44e+00 angle pdb=" C ARG A 336 " pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta sigma weight residual 120.42 116.62 3.80 1.42e+00 4.96e-01 7.16e+00 angle pdb=" C LEU A 108 " pdb=" N VAL A 109 " pdb=" CA VAL A 109 " ideal model delta sigma weight residual 120.46 116.83 3.63 1.37e+00 5.33e-01 7.01e+00 ... (remaining 6834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.36: 2836 28.36 - 56.71: 85 56.71 - 85.07: 8 85.07 - 113.42: 1 113.42 - 141.78: 2 Dihedral angle restraints: 2932 sinusoidal: 1109 harmonic: 1823 Sorted by residual: dihedral pdb=" CA PHE A 251 " pdb=" C PHE A 251 " pdb=" N GLN A 252 " pdb=" CA GLN A 252 " ideal model delta harmonic sigma weight residual 180.00 -153.74 -26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA VAL A 359 " pdb=" C VAL A 359 " pdb=" N GLY A 360 " pdb=" CA GLY A 360 " ideal model delta harmonic sigma weight residual -180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C31 1YI A 701 " pdb=" C29 1YI A 701 " pdb=" C30 1YI A 701 " pdb=" C32 1YI A 701 " ideal model delta sinusoidal sigma weight residual 275.10 133.32 141.78 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 2929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 531 0.042 - 0.084: 221 0.084 - 0.126: 52 0.126 - 0.168: 8 0.168 - 0.210: 5 Chirality restraints: 817 Sorted by residual: chirality pdb=" CA PRO A 324 " pdb=" N PRO A 324 " pdb=" C PRO A 324 " pdb=" CB PRO A 324 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 109 " pdb=" CA VAL A 109 " pdb=" CG1 VAL A 109 " pdb=" CG2 VAL A 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CA ILE A 240 " pdb=" N ILE A 240 " pdb=" C ILE A 240 " pdb=" CB ILE A 240 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 814 not shown) Planarity restraints: 823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 513 " -0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO A 514 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 514 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 514 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 279 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.43e+00 pdb=" C PHE A 279 " -0.047 2.00e-02 2.50e+03 pdb=" O PHE A 279 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE A 280 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 240 " -0.045 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO A 241 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.037 5.00e-02 4.00e+02 ... (remaining 820 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 647 2.75 - 3.29: 5388 3.29 - 3.83: 8471 3.83 - 4.36: 9792 4.36 - 4.90: 17063 Nonbonded interactions: 41361 Sorted by model distance: nonbonded pdb=" OE1 GLN A 142 " pdb=" NZ LYS A 412 " model vdw 2.213 3.120 nonbonded pdb=" NE2 GLN A 142 " pdb=" OD1 ASP A 408 " model vdw 2.214 3.120 nonbonded pdb=" NH1 ARG A 499 " pdb=" OE1 GLU A 503 " model vdw 2.274 3.120 nonbonded pdb=" OH TYR A 462 " pdb=" NH1 ARG A 499 " model vdw 2.274 3.120 nonbonded pdb=" OG SER A 77 " pdb=" OG SER A 396 " model vdw 2.283 3.040 ... (remaining 41356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.810 Find NCS groups from input model: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 : 0.007 0.113 5023 Z= 0.301 Angle : 0.948 8.566 6845 Z= 0.494 Chirality : 0.048 0.210 817 Planarity : 0.008 0.070 823 Dihedral : 13.685 141.779 1757 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.92 % Favored : 94.92 % Rotamer: Outliers : 1.75 % Allowed : 3.51 % Favored : 94.74 % 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: -0.06 (0.33), residues: 630 helix: 0.58 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.55 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 259 TYR 0.017 0.002 TYR A 506 PHE 0.030 0.003 PHE A 168 TRP 0.013 0.002 TRP A 477 HIS 0.004 0.002 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.30 ( 5020) covalent geometry : angle 0.94713 / 0.49 ( 6839) SS BOND : bond 0.00931 / 0.48 ( 3) SS BOND : angle 1.61349 / 0.91 ( 6) hydrogen bonds : bond 0.13677 / 8.95 ( 356) hydrogen bonds : angle 6.68946 / 4.78 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.5944 (mtt90) cc_final: 0.5216 (mtp-110) REVERT: A 163 PHE cc_start: 0.6054 (t80) cc_final: 0.5469 (t80) REVERT: A 202 TYR cc_start: 0.7006 (m-80) cc_final: 0.6637 (m-10) REVERT: A 204 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.5629 (t0) REVERT: A 330 MET cc_start: 0.7763 (mmt) cc_final: 0.7202 (mmt) REVERT: A 374 MET cc_start: 0.7297 (mtp) cc_final: 0.6933 (mtp) REVERT: A 382 MET cc_start: 0.5794 (tpt) cc_final: 0.5395 (mmm) REVERT: A 416 ARG cc_start: 0.7347 (mmm-85) cc_final: 0.6863 (mtm180) REVERT: A 445 GLN cc_start: 0.6498 (tm-30) cc_final: 0.5656 (tt0) REVERT: A 512 MET cc_start: 0.5364 (tpt) cc_final: 0.4620 (tpp) REVERT: A 555 HIS cc_start: 0.8369 (m170) cc_final: 0.7931 (m-70) REVERT: A 630 MET cc_start: 0.6179 (mmm) cc_final: 0.5563 (mpp) REVERT: B 31 MET cc_start: 0.6951 (ttm) cc_final: 0.6133 (tpt) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.0935 time to fit residues: 11.7616 Evaluate side-chains 72 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 324 PRO Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 520 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.209642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.187147 restraints weight = 5644.250| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 1.57 r_work: 0.4036 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5023 Z= 0.168 Angle : 0.700 11.671 6845 Z= 0.359 Chirality : 0.046 0.225 817 Planarity : 0.006 0.054 823 Dihedral : 10.481 122.581 734 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.60 % Favored : 95.24 % Rotamer: Outliers : 0.97 % Allowed : 8.97 % Favored : 90.06 % 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: 0.65 (0.34), residues: 630 helix: 1.10 (0.24), residues: 464 sheet: None (None), residues: 0 loop : -1.41 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 479 TYR 0.013 0.002 TYR A 354 PHE 0.023 0.002 PHE A 168 TRP 0.010 0.001 TRP A 103 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 5020) covalent geometry : angle 0.70033 / 0.36 ( 6839) SS BOND : bond 0.00386 / 0.19 ( 3) SS BOND : angle 0.74873 / 0.39 ( 6) hydrogen bonds : bond 0.05054 / 3.47 ( 356) hydrogen bonds : angle 5.17489 / 3.61 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.6123 (tpp) cc_final: 0.5800 (tpt) REVERT: A 163 PHE cc_start: 0.6015 (t80) cc_final: 0.5690 (t80) REVERT: A 445 GLN cc_start: 0.6595 (tm-30) cc_final: 0.5667 (tt0) REVERT: A 630 MET cc_start: 0.6488 (mmm) cc_final: 0.5794 (mpp) REVERT: B 31 MET cc_start: 0.7731 (ttm) cc_final: 0.7393 (ttm) outliers start: 5 outliers final: 3 residues processed: 79 average time/residue: 0.0751 time to fit residues: 7.6941 Evaluate side-chains 66 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 324 PRO Chi-restraints excluded: chain A residue 355 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.187307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.167702 restraints weight = 5530.180| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.33 r_work: 0.3877 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5023 Z= 0.147 Angle : 0.675 11.016 6845 Z= 0.339 Chirality : 0.045 0.257 817 Planarity : 0.005 0.051 823 Dihedral : 9.587 119.282 726 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.92 % Favored : 94.92 % Rotamer: Outliers : 2.34 % Allowed : 11.50 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.34), residues: 630 helix: 1.32 (0.25), residues: 459 sheet: None (None), residues: 0 loop : -1.39 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.010 0.001 TYR A 354 PHE 0.026 0.002 PHE A 168 TRP 0.008 0.001 TRP A 103 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 5020) covalent geometry : angle 0.67464 / 0.34 ( 6839) SS BOND : bond 0.00250 / 0.12 ( 3) SS BOND : angle 0.64731 / 0.33 ( 6) hydrogen bonds : bond 0.04468 / 3.06 ( 356) hydrogen bonds : angle 4.99311 / 3.48 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.6291 (tpp) cc_final: 0.5970 (tpt) REVERT: A 163 PHE cc_start: 0.5924 (t80) cc_final: 0.5459 (t80) REVERT: A 374 MET cc_start: 0.7206 (mtp) cc_final: 0.6592 (mtp) REVERT: A 414 ARG cc_start: 0.7538 (mtp180) cc_final: 0.6946 (mtm180) REVERT: A 445 GLN cc_start: 0.6392 (tm-30) cc_final: 0.5446 (tt0) REVERT: A 630 MET cc_start: 0.6316 (mmm) cc_final: 0.5705 (mpp) REVERT: B 31 MET cc_start: 0.7706 (ttm) cc_final: 0.7428 (ttm) outliers start: 12 outliers final: 7 residues processed: 74 average time/residue: 0.0576 time to fit residues: 5.6537 Evaluate side-chains 68 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 PRO Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 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 = 0.4149 r_free = 0.4149 target = 0.192531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.173811 restraints weight = 5519.659| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.29 r_work: 0.3889 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5023 Z= 0.135 Angle : 0.644 10.642 6845 Z= 0.324 Chirality : 0.044 0.275 817 Planarity : 0.005 0.049 823 Dihedral : 9.330 120.140 726 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.53 % Allowed : 11.89 % Favored : 85.58 % 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: 1.06 (0.34), residues: 630 helix: 1.50 (0.25), residues: 458 sheet: None (None), residues: 0 loop : -1.49 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.009 0.001 TYR A 526 PHE 0.024 0.001 PHE A 168 TRP 0.007 0.001 TRP A 289 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 5020) covalent geometry : angle 0.64373 / 0.32 ( 6839) SS BOND : bond 0.00231 / 0.11 ( 3) SS BOND : angle 0.57724 / 0.28 ( 6) hydrogen bonds : bond 0.04161 / 2.85 ( 356) hydrogen bonds : angle 4.90201 / 3.40 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.6326 (tpp) cc_final: 0.5975 (tpt) REVERT: A 163 PHE cc_start: 0.5918 (t80) cc_final: 0.5602 (t80) REVERT: A 374 MET cc_start: 0.7170 (mtp) cc_final: 0.6356 (mtp) REVERT: A 445 GLN cc_start: 0.6264 (tm-30) cc_final: 0.5403 (tt0) REVERT: A 452 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.5270 (mm) REVERT: A 630 MET cc_start: 0.6330 (mmm) cc_final: 0.5699 (mpp) REVERT: B 31 MET cc_start: 0.7749 (ttm) cc_final: 0.7485 (ttm) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 0.0688 time to fit residues: 6.5605 Evaluate side-chains 70 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 PRO Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 HIS ** 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 = 0.4360 r_free = 0.4360 target = 0.207525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.184737 restraints weight = 5852.272| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.63 r_work: 0.4014 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5023 Z= 0.147 Angle : 0.661 10.947 6845 Z= 0.332 Chirality : 0.044 0.277 817 Planarity : 0.005 0.047 823 Dihedral : 9.314 118.603 726 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.92 % Allowed : 13.65 % Favored : 83.43 % 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: 1.00 (0.34), residues: 630 helix: 1.49 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.61 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.010 0.002 TYR A 526 PHE 0.024 0.002 PHE A 168 TRP 0.009 0.001 TRP A 641 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 5020) covalent geometry : angle 0.66114 / 0.33 ( 6839) SS BOND : bond 0.00226 / 0.11 ( 3) SS BOND : angle 0.59603 / 0.27 ( 6) hydrogen bonds : bond 0.04286 / 2.94 ( 356) hydrogen bonds : angle 4.91770 / 3.42 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.6229 (tpp) cc_final: 0.5886 (tpt) REVERT: A 48 PHE cc_start: 0.7521 (m-10) cc_final: 0.7218 (m-10) REVERT: A 163 PHE cc_start: 0.5983 (t80) cc_final: 0.5553 (t80) REVERT: A 423 MET cc_start: 0.6078 (mmp) cc_final: 0.5840 (mmp) REVERT: A 445 GLN cc_start: 0.6171 (tm-30) cc_final: 0.5322 (tt0) REVERT: A 452 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.5183 (mm) REVERT: A 630 MET cc_start: 0.6519 (mmm) cc_final: 0.5773 (mpp) REVERT: B 31 MET cc_start: 0.7669 (ttm) cc_final: 0.7349 (ttm) outliers start: 15 outliers final: 8 residues processed: 77 average time/residue: 0.0595 time to fit residues: 5.9641 Evaluate side-chains 72 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 PRO Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 43 optimal weight: 0.0270 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.0370 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 HIS ** 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 = 0.4396 r_free = 0.4396 target = 0.211257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.188574 restraints weight = 5854.163| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 1.63 r_work: 0.4054 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3934 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5023 Z= 0.124 Angle : 0.627 10.404 6845 Z= 0.315 Chirality : 0.043 0.283 817 Planarity : 0.005 0.047 823 Dihedral : 9.029 118.760 726 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.53 % Allowed : 14.23 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.34), residues: 630 helix: 1.68 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -1.51 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.009 0.001 TYR A 526 PHE 0.022 0.001 PHE A 168 TRP 0.006 0.001 TRP A 289 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 5020) covalent geometry : angle 0.62674 / 0.31 ( 6839) SS BOND : bond 0.00196 / 0.10 ( 3) SS BOND : angle 0.59088 / 0.27 ( 6) hydrogen bonds : bond 0.03895 / 2.66 ( 356) hydrogen bonds : angle 4.83134 / 3.34 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.6155 (tpp) cc_final: 0.5833 (tpt) REVERT: A 163 PHE cc_start: 0.6056 (t80) cc_final: 0.5689 (t80) REVERT: A 452 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5204 (mm) REVERT: A 630 MET cc_start: 0.6519 (mmm) cc_final: 0.5808 (mpp) REVERT: B 31 MET cc_start: 0.7649 (ttm) cc_final: 0.7301 (ttm) outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 0.0573 time to fit residues: 5.8396 Evaluate side-chains 71 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 452 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.0170 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 HIS ** 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 = 0.4385 r_free = 0.4385 target = 0.209790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.187183 restraints weight = 5757.383| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 1.60 r_work: 0.4043 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5023 Z= 0.134 Angle : 0.649 10.998 6845 Z= 0.324 Chirality : 0.043 0.279 817 Planarity : 0.005 0.046 823 Dihedral : 8.939 118.277 723 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.31 % Allowed : 14.42 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.34), residues: 630 helix: 1.69 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.65 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.007 0.001 TYR A 191 PHE 0.023 0.001 PHE A 168 TRP 0.007 0.001 TRP A 641 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 5020) covalent geometry : angle 0.64918 / 0.32 ( 6839) SS BOND : bond 0.00194 / 0.10 ( 3) SS BOND : angle 0.52391 / 0.23 ( 6) hydrogen bonds : bond 0.04017 / 2.74 ( 356) hydrogen bonds : angle 4.85109 / 3.36 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.7936 (mm) cc_final: 0.7376 (pt) REVERT: A 40 MET cc_start: 0.6206 (tpp) cc_final: 0.5862 (tpt) REVERT: A 163 PHE cc_start: 0.6185 (t80) cc_final: 0.5729 (t80) REVERT: A 414 ARG cc_start: 0.7355 (mtp180) cc_final: 0.6802 (mtm180) REVERT: A 452 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5185 (mm) REVERT: A 630 MET cc_start: 0.6507 (mmm) cc_final: 0.5786 (mpp) REVERT: B 31 MET cc_start: 0.7656 (ttm) cc_final: 0.7325 (ttm) outliers start: 17 outliers final: 12 residues processed: 75 average time/residue: 0.0626 time to fit residues: 6.1260 Evaluate side-chains 73 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 49 optimal weight: 0.0770 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 HIS ** 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 = 0.4390 r_free = 0.4390 target = 0.210002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.187339 restraints weight = 5834.517| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.62 r_work: 0.4042 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5023 Z= 0.134 Angle : 0.652 11.989 6845 Z= 0.325 Chirality : 0.043 0.297 817 Planarity : 0.005 0.046 823 Dihedral : 8.853 119.291 723 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.51 % Allowed : 15.20 % Favored : 81.29 % 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: 1.33 (0.34), residues: 630 helix: 1.73 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.51 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.007 0.001 TYR A 191 PHE 0.024 0.001 PHE A 168 TRP 0.008 0.001 TRP A 641 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 5020) covalent geometry : angle 0.65168 / 0.33 ( 6839) SS BOND : bond 0.00193 / 0.10 ( 3) SS BOND : angle 0.51341 / 0.22 ( 6) hydrogen bonds : bond 0.03970 / 2.70 ( 356) hydrogen bonds : angle 4.83514 / 3.34 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.7973 (mm) cc_final: 0.7437 (pt) REVERT: A 40 MET cc_start: 0.6179 (tpp) cc_final: 0.5843 (tpt) REVERT: A 48 PHE cc_start: 0.7424 (m-10) cc_final: 0.7075 (m-80) REVERT: A 163 PHE cc_start: 0.6205 (t80) cc_final: 0.5892 (t80) REVERT: A 178 TYR cc_start: 0.4945 (m-80) cc_final: 0.4636 (t80) REVERT: A 414 ARG cc_start: 0.7312 (mtp180) cc_final: 0.6796 (mtm180) REVERT: A 452 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.5235 (mm) REVERT: A 630 MET cc_start: 0.6491 (mmm) cc_final: 0.5765 (mpp) REVERT: B 31 MET cc_start: 0.7668 (ttm) cc_final: 0.7348 (ttm) outliers start: 18 outliers final: 14 residues processed: 77 average time/residue: 0.0568 time to fit residues: 5.7899 Evaluate side-chains 78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 0.0270 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 HIS ** 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 = 0.4398 r_free = 0.4398 target = 0.210807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.188263 restraints weight = 5774.298| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 1.63 r_work: 0.4052 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5023 Z= 0.128 Angle : 0.650 12.699 6845 Z= 0.323 Chirality : 0.043 0.295 817 Planarity : 0.005 0.046 823 Dihedral : 8.765 118.595 723 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.70 % Allowed : 15.20 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.34), residues: 630 helix: 1.80 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.50 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.006 0.001 TYR A 35 PHE 0.023 0.001 PHE A 168 TRP 0.007 0.001 TRP A 289 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 5020) covalent geometry : angle 0.64979 / 0.32 ( 6839) SS BOND : bond 0.00183 / 0.09 ( 3) SS BOND : angle 0.51316 / 0.22 ( 6) hydrogen bonds : bond 0.03865 / 2.64 ( 356) hydrogen bonds : angle 4.81237 / 3.32 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.7988 (mm) cc_final: 0.7428 (pt) REVERT: A 40 MET cc_start: 0.6130 (tpp) cc_final: 0.5742 (tpt) REVERT: A 48 PHE cc_start: 0.7423 (m-10) cc_final: 0.7085 (m-80) REVERT: A 163 PHE cc_start: 0.6126 (t80) cc_final: 0.5901 (t80) REVERT: A 178 TYR cc_start: 0.4911 (m-80) cc_final: 0.4663 (t80) REVERT: A 452 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5237 (mm) REVERT: A 630 MET cc_start: 0.6472 (mmm) cc_final: 0.5752 (mpp) REVERT: B 31 MET cc_start: 0.7693 (ttm) cc_final: 0.7375 (ttm) outliers start: 19 outliers final: 14 residues processed: 79 average time/residue: 0.0622 time to fit residues: 6.5412 Evaluate side-chains 77 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 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 = 0.4385 r_free = 0.4385 target = 0.209359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.186541 restraints weight = 5780.354| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.63 r_work: 0.4034 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5023 Z= 0.138 Angle : 0.661 13.001 6845 Z= 0.327 Chirality : 0.044 0.304 817 Planarity : 0.005 0.046 823 Dihedral : 8.748 118.801 723 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.31 % Allowed : 15.01 % Favored : 81.68 % 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 (0.34), residues: 630 helix: 1.73 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -1.51 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.008 0.001 TYR A 191 PHE 0.026 0.002 PHE A 168 TRP 0.009 0.001 TRP A 641 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 5020) covalent geometry : angle 0.66139 / 0.33 ( 6839) SS BOND : bond 0.00197 / 0.10 ( 3) SS BOND : angle 0.52135 / 0.23 ( 6) hydrogen bonds : bond 0.03968 / 2.72 ( 356) hydrogen bonds : angle 4.81359 / 3.33 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8006 (mm) cc_final: 0.7470 (pt) REVERT: A 40 MET cc_start: 0.6206 (tpp) cc_final: 0.5807 (tpt) REVERT: A 48 PHE cc_start: 0.7485 (m-10) cc_final: 0.7240 (m-10) REVERT: A 163 PHE cc_start: 0.6288 (t80) cc_final: 0.6037 (t80) REVERT: A 178 TYR cc_start: 0.4922 (m-80) cc_final: 0.4586 (t80) REVERT: A 452 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5269 (mm) REVERT: A 477 TRP cc_start: 0.6975 (t-100) cc_final: 0.6361 (t-100) REVERT: A 630 MET cc_start: 0.6511 (mmm) cc_final: 0.5778 (mpp) REVERT: B 31 MET cc_start: 0.7663 (ttm) cc_final: 0.7344 (ttm) outliers start: 17 outliers final: 15 residues processed: 78 average time/residue: 0.0552 time to fit residues: 5.7151 Evaluate side-chains 78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 517 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.0020 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 HIS ** 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 = 0.4388 r_free = 0.4388 target = 0.209289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.187979 restraints weight = 5744.019| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 1.53 r_work: 0.4071 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5023 Z= 0.125 Angle : 0.646 13.376 6845 Z= 0.320 Chirality : 0.043 0.287 817 Planarity : 0.005 0.046 823 Dihedral : 8.648 118.886 723 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.31 % Allowed : 14.81 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.34), residues: 630 helix: 1.80 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -1.58 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.006 0.001 TYR A 35 PHE 0.023 0.001 PHE A 168 TRP 0.007 0.001 TRP A 289 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 5020) covalent geometry : angle 0.64572 / 0.32 ( 6839) SS BOND : bond 0.00179 / 0.09 ( 3) SS BOND : angle 0.52555 / 0.23 ( 6) hydrogen bonds : bond 0.03776 / 2.57 ( 356) hydrogen bonds : angle 4.79140 / 3.31 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1212.57 seconds wall clock time: 21 minutes 29.46 seconds (1289.46 seconds total)