Starting phenix.real_space_refine on Fri Dec 27 11:10:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yni_33962/12_2024/7yni_33962.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yni_33962/12_2024/7yni_33962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yni_33962/12_2024/7yni_33962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yni_33962/12_2024/7yni_33962.map" model { file = "/net/cci-nas-00/data/ceres_data/7yni_33962/12_2024/7yni_33962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yni_33962/12_2024/7yni_33962.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.009 sd= 0.146 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 32 5.16 5 C 2926 2.51 5 N 694 2.21 5 O 734 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4387 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4182 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 21, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "B" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 193 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'KQC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.18, per 1000 atoms: 0.72 Number of scatterers: 4387 At special positions: 0 Unit cell: (85.068, 75.06, 77.562, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 F 1 9.00 O 734 8.00 N 694 7.00 C 2926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.04 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " 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: 1.27 Conformation dependent library (CDL) restraints added in 573.1 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 83.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 21 through 24 Processing helix chain 'A' and resid 25 through 48 removed outlier: 3.594A pdb=" N ILE A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 80 through 94 Processing helix chain 'A' and resid 96 through 115 removed outlier: 3.609A pdb=" N GLY A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 107 " --> pdb=" O TRP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 139 through 173 removed outlier: 4.477A pdb=" N ILE A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 201 through 227 Processing helix chain 'A' and resid 227 through 237 removed outlier: 4.017A pdb=" N ALA A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.837A pdb=" N TYR A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 293 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.506A pdb=" N VAL A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 323 through 339 removed outlier: 4.696A pdb=" N MET A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 356 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 373 Processing helix chain 'A' and resid 375 through 409 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 418 through 445 Proline residue: A 442 - end of helix removed outlier: 3.641A pdb=" N GLN A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 464 through 477 Processing helix chain 'A' and resid 481 through 507 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 525 through 548 removed outlier: 3.729A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 Processing helix chain 'A' and resid 638 through 663 Processing helix chain 'B' and resid 28 through 54 Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 246 355 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: 1.29 Time building geometry restraints manager: 1.42 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: 1215 1.34 - 1.45: 776 1.45 - 1.57: 2452 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 4494 Sorted by residual: bond pdb=" C1 KQC A 701 " pdb=" O1 KQC A 701 " ideal model delta sigma weight residual 1.375 1.432 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CA VAL A 441 " pdb=" C VAL A 441 " ideal model delta sigma weight residual 1.524 1.502 0.023 1.11e-02 8.12e+03 4.12e+00 bond pdb=" N VAL A 441 " pdb=" CA VAL A 441 " ideal model delta sigma weight residual 1.463 1.486 -0.023 1.18e-02 7.18e+03 3.85e+00 bond pdb=" CA TYR A 366 " pdb=" C TYR A 366 " ideal model delta sigma weight residual 1.520 1.500 0.021 1.23e-02 6.61e+03 2.80e+00 bond pdb=" C LEU A 387 " pdb=" O LEU A 387 " ideal model delta sigma weight residual 1.237 1.218 0.018 1.17e-02 7.31e+03 2.48e+00 ... (remaining 4489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 5925 1.48 - 2.95: 171 2.95 - 4.43: 34 4.43 - 5.90: 14 5.90 - 7.38: 2 Bond angle restraints: 6146 Sorted by residual: angle pdb=" N ARG A 135 " pdb=" CA ARG A 135 " pdb=" C ARG A 135 " ideal model delta sigma weight residual 111.36 117.03 -5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" N PRO A 552 " pdb=" CA PRO A 552 " pdb=" C PRO A 552 " ideal model delta sigma weight residual 112.47 118.72 -6.25 2.06e+00 2.36e-01 9.21e+00 angle pdb=" N VAL A 441 " pdb=" CA VAL A 441 " pdb=" CB VAL A 441 " ideal model delta sigma weight residual 110.52 108.56 1.96 6.70e-01 2.23e+00 8.58e+00 angle pdb=" CA TRP A 68 " pdb=" CB TRP A 68 " pdb=" CG TRP A 68 " ideal model delta sigma weight residual 113.60 119.11 -5.51 1.90e+00 2.77e-01 8.41e+00 angle pdb=" C ILE A 364 " pdb=" CA ILE A 364 " pdb=" CB ILE A 364 " ideal model delta sigma weight residual 112.19 109.29 2.90 1.15e+00 7.56e-01 6.37e+00 ... (remaining 6141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 2427 15.76 - 31.52: 131 31.52 - 47.28: 32 47.28 - 63.04: 3 63.04 - 78.80: 3 Dihedral angle restraints: 2596 sinusoidal: 886 harmonic: 1710 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -135.79 49.79 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 133.53 -40.53 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CB CYS A 345 " pdb=" SG CYS A 345 " pdb=" SG CYS A 351 " pdb=" CB CYS A 351 " ideal model delta sinusoidal sigma weight residual 93.00 126.08 -33.08 1 1.00e+01 1.00e-02 1.56e+01 ... (remaining 2593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 540 0.039 - 0.078: 163 0.078 - 0.117: 47 0.117 - 0.156: 8 0.156 - 0.195: 3 Chirality restraints: 761 Sorted by residual: chirality pdb=" CA PRO A 552 " pdb=" N PRO A 552 " pdb=" C PRO A 552 " pdb=" CB PRO A 552 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA ARG A 135 " pdb=" N ARG A 135 " pdb=" C ARG A 135 " pdb=" CB ARG A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.16e-01 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 2.56 0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 758 not shown) Planarity restraints: 734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 154 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE A 154 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE A 154 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 155 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 155 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C PHE A 155 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE A 155 " -0.022 2.00e-02 2.50e+03 pdb=" N THR A 156 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 551 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 552 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 552 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 552 " -0.036 5.00e-02 4.00e+02 ... (remaining 731 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 602 2.75 - 3.28: 4879 3.28 - 3.82: 7903 3.82 - 4.36: 8927 4.36 - 4.90: 15620 Nonbonded interactions: 37931 Sorted by model distance: nonbonded pdb=" NE2 HIS A 83 " pdb=" O1 KQC A 701 " model vdw 2.206 3.120 nonbonded pdb=" NE2 GLN A 207 " pdb=" CA ALA A 388 " model vdw 2.233 3.550 nonbonded pdb=" OH TYR A 35 " pdb=" NE2 GLN A 207 " model vdw 2.287 3.120 nonbonded pdb=" OH TYR A 557 " pdb=" OE1 GLU A 568 " model vdw 2.295 3.040 nonbonded pdb=" O GLN A 448 " pdb=" OG SER A 449 " model vdw 2.296 3.040 ... (remaining 37926 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4494 Z= 0.290 Angle : 0.661 7.378 6146 Z= 0.374 Chirality : 0.042 0.195 761 Planarity : 0.006 0.067 734 Dihedral : 10.917 78.797 1487 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.98 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.35), residues: 582 helix: 1.18 (0.24), residues: 442 sheet: None (None), residues: 0 loop : -1.54 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 68 HIS 0.005 0.001 HIS A 83 PHE 0.011 0.002 PHE A 663 TYR 0.020 0.002 TYR A 144 ARG 0.009 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.7696 (tpt) cc_final: 0.7003 (tpt) REVERT: A 328 MET cc_start: 0.7002 (mtt) cc_final: 0.5502 (mtt) REVERT: A 526 TYR cc_start: 0.6157 (p90) cc_final: 0.4766 (p90) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1822 time to fit residues: 11.3355 Evaluate side-chains 43 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4494 Z= 0.286 Angle : 0.693 7.463 6146 Z= 0.362 Chirality : 0.046 0.209 761 Planarity : 0.006 0.062 734 Dihedral : 4.585 20.783 646 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.64 % Favored : 94.85 % Rotamer: Outliers : 0.70 % Allowed : 5.81 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.35), residues: 582 helix: 1.32 (0.24), residues: 450 sheet: None (None), residues: 0 loop : -1.39 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 30 HIS 0.008 0.002 HIS A 83 PHE 0.017 0.002 PHE A 663 TYR 0.013 0.002 TYR A 236 ARG 0.005 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.441 Fit side-chains REVERT: A 233 MET cc_start: 0.6668 (mtm) cc_final: 0.6430 (mtm) REVERT: A 283 MET cc_start: 0.7718 (tpt) cc_final: 0.6763 (tpt) REVERT: A 300 ARG cc_start: 0.7054 (mpt180) cc_final: 0.6354 (mpt180) REVERT: A 328 MET cc_start: 0.6822 (mtt) cc_final: 0.5593 (mtt) REVERT: A 501 ILE cc_start: 0.7441 (mm) cc_final: 0.7224 (mm) REVERT: A 632 MET cc_start: 0.7055 (tpp) cc_final: 0.6853 (mpp) outliers start: 3 outliers final: 1 residues processed: 48 average time/residue: 0.1586 time to fit residues: 10.2746 Evaluate side-chains 44 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4494 Z= 0.238 Angle : 0.637 7.229 6146 Z= 0.334 Chirality : 0.044 0.217 761 Planarity : 0.006 0.057 734 Dihedral : 4.397 19.841 646 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.47 % Favored : 95.02 % Rotamer: Outliers : 1.40 % Allowed : 9.30 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.35), residues: 582 helix: 1.48 (0.24), residues: 450 sheet: None (None), residues: 0 loop : -1.42 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 30 HIS 0.005 0.001 HIS A 83 PHE 0.014 0.001 PHE A 232 TYR 0.011 0.001 TYR A 236 ARG 0.004 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 233 MET cc_start: 0.6631 (mtm) cc_final: 0.6360 (mtm) REVERT: A 283 MET cc_start: 0.7699 (tpt) cc_final: 0.6872 (tpt) REVERT: A 300 ARG cc_start: 0.7146 (mpt180) cc_final: 0.6605 (mpt180) REVERT: A 328 MET cc_start: 0.7031 (mtt) cc_final: 0.5689 (mtt) REVERT: A 501 ILE cc_start: 0.7401 (mm) cc_final: 0.7145 (mm) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.1732 time to fit residues: 10.4316 Evaluate side-chains 45 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4494 Z= 0.241 Angle : 0.616 7.275 6146 Z= 0.326 Chirality : 0.043 0.218 761 Planarity : 0.006 0.057 734 Dihedral : 4.287 18.838 646 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.33 % Favored : 94.16 % Rotamer: Outliers : 2.09 % Allowed : 11.16 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.36), residues: 582 helix: 1.58 (0.24), residues: 449 sheet: None (None), residues: 0 loop : -1.57 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 30 HIS 0.004 0.001 HIS A 83 PHE 0.016 0.001 PHE A 232 TYR 0.010 0.001 TYR A 236 ARG 0.004 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 233 MET cc_start: 0.6662 (mtm) cc_final: 0.6412 (mtm) REVERT: A 300 ARG cc_start: 0.7098 (mpt180) cc_final: 0.6626 (mpt180) REVERT: A 328 MET cc_start: 0.7162 (mtt) cc_final: 0.6062 (mtt) REVERT: A 501 ILE cc_start: 0.7249 (mm) cc_final: 0.6980 (mm) outliers start: 9 outliers final: 5 residues processed: 49 average time/residue: 0.1274 time to fit residues: 8.6493 Evaluate side-chains 47 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4494 Z= 0.291 Angle : 0.642 7.275 6146 Z= 0.339 Chirality : 0.044 0.216 761 Planarity : 0.006 0.060 734 Dihedral : 4.318 18.736 646 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.33 % Favored : 94.16 % Rotamer: Outliers : 2.09 % Allowed : 13.95 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.35), residues: 582 helix: 1.41 (0.24), residues: 450 sheet: None (None), residues: 0 loop : -1.65 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 30 HIS 0.004 0.001 HIS A 83 PHE 0.016 0.001 PHE A 232 TYR 0.012 0.001 TYR A 236 ARG 0.004 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 233 MET cc_start: 0.6719 (mtm) cc_final: 0.6427 (mtm) REVERT: A 300 ARG cc_start: 0.7127 (mpt180) cc_final: 0.6588 (mpt180) REVERT: A 328 MET cc_start: 0.7283 (mtt) cc_final: 0.6220 (mtt) REVERT: A 501 ILE cc_start: 0.7246 (mm) cc_final: 0.6959 (mm) outliers start: 9 outliers final: 7 residues processed: 46 average time/residue: 0.1362 time to fit residues: 8.8030 Evaluate side-chains 48 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4494 Z= 0.227 Angle : 0.604 7.230 6146 Z= 0.319 Chirality : 0.042 0.215 761 Planarity : 0.006 0.058 734 Dihedral : 4.206 17.704 646 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.15 % Favored : 94.33 % Rotamer: Outliers : 2.56 % Allowed : 14.42 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.36), residues: 582 helix: 1.60 (0.24), residues: 450 sheet: None (None), residues: 0 loop : -1.63 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 30 HIS 0.003 0.001 HIS A 83 PHE 0.015 0.001 PHE A 232 TYR 0.010 0.001 TYR A 236 ARG 0.003 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.500 Fit side-chains REVERT: A 233 MET cc_start: 0.6663 (mtm) cc_final: 0.6361 (mtm) REVERT: A 300 ARG cc_start: 0.7067 (mpt180) cc_final: 0.6683 (mpt180) REVERT: A 325 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6921 (ttt) REVERT: A 328 MET cc_start: 0.7072 (mtt) cc_final: 0.6197 (mtt) REVERT: A 501 ILE cc_start: 0.7239 (mm) cc_final: 0.6942 (mm) outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 0.1394 time to fit residues: 9.8310 Evaluate side-chains 50 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4494 Z= 0.224 Angle : 0.612 7.206 6146 Z= 0.319 Chirality : 0.042 0.216 761 Planarity : 0.006 0.058 734 Dihedral : 4.200 17.150 646 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.81 % Favored : 94.67 % Rotamer: Outliers : 2.56 % Allowed : 16.05 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.36), residues: 582 helix: 1.58 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -1.60 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 30 HIS 0.003 0.001 HIS A 83 PHE 0.015 0.001 PHE A 232 TYR 0.010 0.001 TYR A 236 ARG 0.002 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.421 Fit side-chains REVERT: A 233 MET cc_start: 0.6676 (mtm) cc_final: 0.6381 (mtm) REVERT: A 283 MET cc_start: 0.7755 (tpt) cc_final: 0.7163 (tpt) REVERT: A 300 ARG cc_start: 0.7076 (mpt180) cc_final: 0.6683 (mpt180) REVERT: A 328 MET cc_start: 0.7015 (mtt) cc_final: 0.6281 (mtt) REVERT: A 501 ILE cc_start: 0.7247 (mm) cc_final: 0.6953 (mm) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 0.1324 time to fit residues: 9.5991 Evaluate side-chains 51 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4494 Z= 0.268 Angle : 0.640 7.473 6146 Z= 0.333 Chirality : 0.044 0.212 761 Planarity : 0.006 0.060 734 Dihedral : 4.263 17.318 646 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.15 % Favored : 94.33 % Rotamer: Outliers : 2.09 % Allowed : 15.35 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.35), residues: 582 helix: 1.51 (0.24), residues: 449 sheet: None (None), residues: 0 loop : -1.76 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 30 HIS 0.004 0.001 HIS A 83 PHE 0.016 0.001 PHE A 232 TYR 0.011 0.001 TYR A 236 ARG 0.003 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.395 Fit side-chains REVERT: A 233 MET cc_start: 0.6714 (mtm) cc_final: 0.6413 (mtm) REVERT: A 300 ARG cc_start: 0.7107 (mpt180) cc_final: 0.6692 (mpt180) REVERT: A 328 MET cc_start: 0.7064 (mtt) cc_final: 0.6348 (mtt) REVERT: A 501 ILE cc_start: 0.7250 (mm) cc_final: 0.6945 (mm) outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 0.1442 time to fit residues: 9.2118 Evaluate side-chains 50 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 26 optimal weight: 0.0170 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4494 Z= 0.210 Angle : 0.616 7.191 6146 Z= 0.320 Chirality : 0.042 0.215 761 Planarity : 0.006 0.058 734 Dihedral : 4.228 21.381 646 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.64 % Favored : 95.02 % Rotamer: Outliers : 1.63 % Allowed : 16.05 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.36), residues: 582 helix: 1.72 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -1.77 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 30 HIS 0.003 0.001 HIS A 83 PHE 0.014 0.001 PHE A 232 TYR 0.010 0.001 TYR A 236 ARG 0.002 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.429 Fit side-chains REVERT: A 233 MET cc_start: 0.6658 (mtm) cc_final: 0.6359 (mtm) REVERT: A 283 MET cc_start: 0.7679 (tpt) cc_final: 0.7160 (tpt) REVERT: A 300 ARG cc_start: 0.7040 (mpt180) cc_final: 0.6746 (mpt180) REVERT: A 328 MET cc_start: 0.6962 (mtt) cc_final: 0.6314 (mtt) REVERT: A 501 ILE cc_start: 0.7241 (mm) cc_final: 0.6943 (mm) outliers start: 7 outliers final: 7 residues processed: 50 average time/residue: 0.1468 time to fit residues: 9.9105 Evaluate side-chains 51 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.0070 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4494 Z= 0.203 Angle : 0.625 9.794 6146 Z= 0.322 Chirality : 0.042 0.217 761 Planarity : 0.006 0.058 734 Dihedral : 4.199 19.586 646 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.81 % Favored : 94.85 % Rotamer: Outliers : 1.86 % Allowed : 16.51 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.36), residues: 582 helix: 1.75 (0.25), residues: 450 sheet: None (None), residues: 0 loop : -1.71 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 30 HIS 0.003 0.001 HIS A 83 PHE 0.014 0.001 PHE A 232 TYR 0.015 0.001 TYR A 256 ARG 0.006 0.001 ARG A 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.422 Fit side-chains REVERT: A 233 MET cc_start: 0.6606 (mtm) cc_final: 0.6316 (mtm) REVERT: A 283 MET cc_start: 0.7660 (tpt) cc_final: 0.7138 (tpt) REVERT: A 300 ARG cc_start: 0.7028 (mpt180) cc_final: 0.6775 (mpt180) REVERT: A 328 MET cc_start: 0.6941 (mtt) cc_final: 0.6304 (mtt) REVERT: A 501 ILE cc_start: 0.7233 (mm) cc_final: 0.6936 (mm) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.1471 time to fit residues: 10.2852 Evaluate side-chains 49 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.0670 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.190474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.160824 restraints weight = 4144.790| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.66 r_work: 0.3873 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4494 Z= 0.208 Angle : 0.621 9.731 6146 Z= 0.321 Chirality : 0.043 0.223 761 Planarity : 0.006 0.059 734 Dihedral : 4.170 19.864 646 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.81 % Favored : 94.85 % Rotamer: Outliers : 1.86 % Allowed : 16.51 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.36), residues: 582 helix: 1.77 (0.25), residues: 450 sheet: None (None), residues: 0 loop : -1.69 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 30 HIS 0.003 0.001 HIS A 83 PHE 0.014 0.001 PHE A 232 TYR 0.013 0.001 TYR A 256 ARG 0.005 0.001 ARG A 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1225.72 seconds wall clock time: 22 minutes 58.53 seconds (1378.53 seconds total)