Starting phenix.real_space_refine on Fri Dec 27 06:49:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8erq_28558/12_2024/8erq_28558.cif Found real_map, /net/cci-nas-00/data/ceres_data/8erq_28558/12_2024/8erq_28558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8erq_28558/12_2024/8erq_28558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8erq_28558/12_2024/8erq_28558.map" model { file = "/net/cci-nas-00/data/ceres_data/8erq_28558/12_2024/8erq_28558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8erq_28558/12_2024/8erq_28558.cif" } resolution = 3.3 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= -0.002 sd= 0.049 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 15 5.16 5 C 2040 2.51 5 N 534 2.21 5 O 589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3178 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 866 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 110} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 778 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1520 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 12, 'TRANS': 184} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.25, per 1000 atoms: 1.65 Number of scatterers: 3178 At special positions: 0 Unit cell: (86, 62, 96, 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 15 16.00 O 589 8.00 N 534 7.00 C 2040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.07 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.21 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.12 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 449.4 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 9.2% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'L' and resid 82 through 86 removed outlier: 4.054A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.742A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.897A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 370' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.648A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.704A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.583A pdb=" N VAL L 11 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN L 40 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.583A pdb=" N VAL L 11 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.848A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.736A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 110 hydrogen bonds defined for protein. 258 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: 0.78 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 909 1.33 - 1.46: 947 1.46 - 1.59: 1387 1.59 - 1.73: 0 1.73 - 1.86: 18 Bond restraints: 3261 Sorted by residual: bond pdb=" CB ILE H 2 " pdb=" CG1 ILE H 2 " ideal model delta sigma weight residual 1.530 1.588 -0.058 2.00e-02 2.50e+03 8.42e+00 bond pdb=" NE ARG L 64 " pdb=" CZ ARG L 64 " ideal model delta sigma weight residual 1.326 1.357 -0.031 1.10e-02 8.26e+03 7.93e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.465 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" CD GLU H 6 " pdb=" OE1 GLU H 6 " ideal model delta sigma weight residual 1.249 1.200 0.049 1.90e-02 2.77e+03 6.60e+00 bond pdb=" CG ASP L 88 " pdb=" OD1 ASP L 88 " ideal model delta sigma weight residual 1.249 1.201 0.048 1.90e-02 2.77e+03 6.39e+00 ... (remaining 3256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 4387 3.99 - 7.97: 65 7.97 - 11.96: 2 11.96 - 15.95: 0 15.95 - 19.94: 2 Bond angle restraints: 4456 Sorted by residual: angle pdb=" CG1 VAL A 503 " pdb=" CB VAL A 503 " pdb=" CG2 VAL A 503 " ideal model delta sigma weight residual 110.80 130.74 -19.94 2.20e+00 2.07e-01 8.21e+01 angle pdb=" C ARG A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 127.58 -8.02 1.02e+00 9.61e-01 6.19e+01 angle pdb=" C GLN H 41 " pdb=" N PRO H 42 " pdb=" CA PRO H 42 " ideal model delta sigma weight residual 119.66 124.99 -5.33 7.20e-01 1.93e+00 5.48e+01 angle pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 119.56 126.75 -7.19 1.02e+00 9.61e-01 4.97e+01 angle pdb=" C ARG L 57 " pdb=" N PRO L 58 " pdb=" CA PRO L 58 " ideal model delta sigma weight residual 120.03 126.67 -6.64 9.90e-01 1.02e+00 4.50e+01 ... (remaining 4451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 1818 15.37 - 30.75: 78 30.75 - 46.12: 26 46.12 - 61.50: 8 61.50 - 76.87: 1 Dihedral angle restraints: 1931 sinusoidal: 701 harmonic: 1230 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -40.27 -45.73 1 1.00e+01 1.00e-02 2.90e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 50.76 42.24 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CA ALA A 372 " pdb=" C ALA A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 1928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 458 0.109 - 0.218: 42 0.218 - 0.327: 1 0.327 - 0.436: 0 0.436 - 0.546: 2 Chirality restraints: 503 Sorted by residual: chirality pdb=" CG LEU A 368 " pdb=" CB LEU A 368 " pdb=" CD1 LEU A 368 " pdb=" CD2 LEU A 368 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" CB VAL A 503 " pdb=" CA VAL A 503 " pdb=" CG1 VAL A 503 " pdb=" CG2 VAL A 503 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" C2 NAG A1301 " pdb=" C1 NAG A1301 " pdb=" C3 NAG A1301 " pdb=" N2 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.82 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 500 not shown) Planarity restraints: 571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 516 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C GLU A 516 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU A 516 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 517 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 366 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C SER A 366 " 0.036 2.00e-02 2.50e+03 pdb=" O SER A 366 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 367 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 371 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C LEU A 371 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 371 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 372 " 0.011 2.00e-02 2.50e+03 ... (remaining 568 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 768 2.79 - 3.32: 2533 3.32 - 3.85: 5041 3.85 - 4.37: 5896 4.37 - 4.90: 10338 Nonbonded interactions: 24576 Sorted by model distance: nonbonded pdb=" CD1 PHE A 392 " pdb=" CD2 LEU A 517 " model vdw 2.265 3.760 nonbonded pdb=" OD2 ASP H 58 " pdb=" NZ LYS A 444 " model vdw 2.385 3.120 nonbonded pdb=" OG1 THR H 21 " pdb=" NE2 GLN H 79 " model vdw 2.532 3.120 nonbonded pdb=" N ASP A 389 " pdb=" N LEU A 390 " model vdw 2.587 2.560 nonbonded pdb=" O SER A 496 " pdb=" OG SER A 496 " model vdw 2.590 3.040 ... (remaining 24571 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: 6.460 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: 0.020 Set scattering table: 0.030 Process input model: 14.780 Find NCS groups from input model: 0.040 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.010 0.058 3261 Z= 0.712 Angle : 1.320 19.937 4456 Z= 0.872 Chirality : 0.072 0.546 503 Planarity : 0.005 0.024 570 Dihedral : 10.042 76.869 1131 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.95 % Allowed : 1.90 % Favored : 97.15 % 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: 0.38 (0.42), residues: 417 helix: -4.49 (0.46), residues: 26 sheet: 1.12 (0.43), residues: 146 loop : 0.36 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP H 109 HIS 0.001 0.000 HIS L 42 PHE 0.021 0.003 PHE A 374 TYR 0.021 0.004 TYR L 33 ARG 0.003 0.001 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.353 Fit side-chains REVERT: H 17 THR cc_start: 0.6166 (m) cc_final: 0.5902 (p) outliers start: 3 outliers final: 0 residues processed: 75 average time/residue: 0.1989 time to fit residues: 17.6203 Evaluate side-chains 49 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN L 40 GLN L 41 HIS L 42 HIS A 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3261 Z= 0.237 Angle : 0.612 10.672 4456 Z= 0.314 Chirality : 0.046 0.158 503 Planarity : 0.005 0.046 570 Dihedral : 4.481 20.745 486 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.06 % Allowed : 8.23 % Favored : 86.71 % 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: 0.50 (0.43), residues: 417 helix: -3.96 (0.78), residues: 26 sheet: 1.43 (0.44), residues: 144 loop : 0.23 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.002 0.001 HIS H 100 PHE 0.011 0.002 PHE H 24 TYR 0.011 0.001 TYR L 39 ARG 0.005 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.335 Fit side-chains REVERT: H 17 THR cc_start: 0.6086 (m) cc_final: 0.5873 (p) REVERT: L 63 ASN cc_start: 0.7211 (t0) cc_final: 0.6911 (t0) REVERT: A 469 SER cc_start: 0.8825 (m) cc_final: 0.8620 (p) outliers start: 16 outliers final: 9 residues processed: 65 average time/residue: 0.1356 time to fit residues: 11.0080 Evaluate side-chains 60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0050 chunk 24 optimal weight: 0.0570 chunk 10 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.0040 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3261 Z= 0.170 Angle : 0.545 7.720 4456 Z= 0.278 Chirality : 0.044 0.139 503 Planarity : 0.004 0.049 570 Dihedral : 4.165 19.204 486 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.80 % Allowed : 10.44 % Favored : 85.76 % 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: 0.33 (0.43), residues: 417 helix: -3.96 (0.73), residues: 26 sheet: 1.35 (0.45), residues: 144 loop : 0.06 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS L 41 PHE 0.011 0.001 PHE A 456 TYR 0.012 0.001 TYR H 54 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.321 Fit side-chains REVERT: H 54 TYR cc_start: 0.8811 (m-80) cc_final: 0.8596 (m-80) REVERT: L 108 THR cc_start: 0.7444 (t) cc_final: 0.7021 (p) outliers start: 12 outliers final: 8 residues processed: 57 average time/residue: 0.1304 time to fit residues: 9.4294 Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN A 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3261 Z= 0.345 Angle : 0.646 9.780 4456 Z= 0.323 Chirality : 0.048 0.162 503 Planarity : 0.005 0.051 570 Dihedral : 4.766 19.784 486 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.11 % Allowed : 11.08 % Favored : 84.81 % 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: -0.07 (0.42), residues: 417 helix: -4.28 (0.57), residues: 26 sheet: 1.06 (0.43), residues: 151 loop : -0.24 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.003 0.001 HIS L 42 PHE 0.016 0.002 PHE A 377 TYR 0.015 0.002 TYR L 89 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.360 Fit side-chains REVERT: L 108 THR cc_start: 0.7959 (t) cc_final: 0.7648 (p) REVERT: A 468 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7830 (pt) outliers start: 13 outliers final: 7 residues processed: 47 average time/residue: 0.1462 time to fit residues: 8.6829 Evaluate side-chains 44 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.0040 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.0570 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN A 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3261 Z= 0.238 Angle : 0.561 7.780 4456 Z= 0.283 Chirality : 0.045 0.137 503 Planarity : 0.005 0.054 570 Dihedral : 4.453 19.389 486 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.11 % Allowed : 10.44 % Favored : 85.44 % 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: 0.10 (0.43), residues: 417 helix: -4.14 (0.74), residues: 18 sheet: 1.12 (0.44), residues: 146 loop : -0.22 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS A 505 PHE 0.010 0.001 PHE H 24 TYR 0.011 0.001 TYR L 89 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.346 Fit side-chains REVERT: L 108 THR cc_start: 0.7963 (t) cc_final: 0.7630 (p) REVERT: A 468 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7885 (pt) outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 0.1716 time to fit residues: 10.9178 Evaluate side-chains 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 28 optimal weight: 0.3980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3261 Z= 0.243 Angle : 0.568 8.136 4456 Z= 0.283 Chirality : 0.045 0.136 503 Planarity : 0.005 0.054 570 Dihedral : 4.482 19.982 486 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.75 % Allowed : 12.03 % Favored : 83.23 % 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: 0.04 (0.43), residues: 417 helix: -4.45 (0.77), residues: 12 sheet: 1.10 (0.45), residues: 144 loop : -0.36 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS A 505 PHE 0.010 0.001 PHE A 377 TYR 0.010 0.001 TYR L 89 ARG 0.003 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.370 Fit side-chains REVERT: A 468 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7846 (pt) outliers start: 15 outliers final: 10 residues processed: 49 average time/residue: 0.1317 time to fit residues: 8.3292 Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3261 Z= 0.237 Angle : 0.559 8.337 4456 Z= 0.278 Chirality : 0.045 0.133 503 Planarity : 0.005 0.054 570 Dihedral : 4.465 20.612 486 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.06 % Allowed : 12.34 % Favored : 82.59 % 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: -0.03 (0.42), residues: 417 helix: -4.35 (0.84), residues: 12 sheet: 1.13 (0.45), residues: 144 loop : -0.47 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS A 505 PHE 0.010 0.001 PHE A 377 TYR 0.009 0.001 TYR L 89 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.452 Fit side-chains REVERT: A 468 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7865 (pt) outliers start: 16 outliers final: 12 residues processed: 52 average time/residue: 0.1449 time to fit residues: 9.7138 Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 11 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3261 Z= 0.234 Angle : 0.561 8.180 4456 Z= 0.279 Chirality : 0.045 0.164 503 Planarity : 0.005 0.054 570 Dihedral : 4.478 21.268 486 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.43 % Allowed : 12.97 % Favored : 82.59 % 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: -0.03 (0.43), residues: 417 helix: -4.37 (0.81), residues: 12 sheet: 1.17 (0.45), residues: 144 loop : -0.50 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS A 505 PHE 0.009 0.001 PHE A 377 TYR 0.009 0.001 TYR L 89 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.372 Fit side-chains REVERT: A 386 LYS cc_start: 0.7983 (mttt) cc_final: 0.6660 (pttt) REVERT: A 468 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7867 (pt) outliers start: 14 outliers final: 12 residues processed: 49 average time/residue: 0.1616 time to fit residues: 9.8041 Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 18 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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: 0.7793 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3261 Z= 0.176 Angle : 0.525 7.059 4456 Z= 0.262 Chirality : 0.045 0.159 503 Planarity : 0.004 0.053 570 Dihedral : 4.310 20.688 486 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.75 % Allowed : 12.66 % Favored : 82.59 % 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: -0.03 (0.42), residues: 417 helix: -4.36 (0.80), residues: 12 sheet: 1.44 (0.46), residues: 134 loop : -0.60 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS A 505 PHE 0.007 0.001 PHE A 377 TYR 0.010 0.001 TYR L 39 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.412 Fit side-chains REVERT: A 386 LYS cc_start: 0.7950 (mttt) cc_final: 0.6663 (pttt) REVERT: A 468 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7803 (pt) outliers start: 15 outliers final: 11 residues processed: 51 average time/residue: 0.1662 time to fit residues: 10.4574 Evaluate side-chains 58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.0020 chunk 8 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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: 0.7807 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3261 Z= 0.214 Angle : 0.566 8.167 4456 Z= 0.275 Chirality : 0.046 0.159 503 Planarity : 0.004 0.053 570 Dihedral : 4.372 20.536 486 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.43 % Allowed : 12.66 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.42), residues: 417 helix: -4.36 (0.78), residues: 12 sheet: 1.45 (0.46), residues: 134 loop : -0.69 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS A 505 PHE 0.008 0.001 PHE A 377 TYR 0.009 0.001 TYR L 39 ARG 0.003 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.307 Fit side-chains REVERT: A 386 LYS cc_start: 0.7945 (mttt) cc_final: 0.6652 (pttt) REVERT: A 468 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7873 (pt) outliers start: 14 outliers final: 12 residues processed: 54 average time/residue: 0.1471 time to fit residues: 10.2079 Evaluate side-chains 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.2980 chunk 36 optimal weight: 0.2980 chunk 21 optimal weight: 0.1980 chunk 27 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 14 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.157524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133139 restraints weight = 3810.799| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.91 r_work: 0.3249 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3261 Z= 0.183 Angle : 0.543 8.495 4456 Z= 0.265 Chirality : 0.045 0.147 503 Planarity : 0.004 0.053 570 Dihedral : 4.282 20.328 486 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.11 % Allowed : 14.24 % Favored : 81.65 % 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: -0.08 (0.42), residues: 417 helix: -4.26 (0.81), residues: 12 sheet: 1.46 (0.46), residues: 134 loop : -0.68 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS A 505 PHE 0.007 0.001 PHE H 24 TYR 0.009 0.001 TYR L 39 ARG 0.003 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1597.03 seconds wall clock time: 29 minutes 44.57 seconds (1784.57 seconds total)