Starting phenix.real_space_refine on Tue Sep 24 00:41:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x95_33067/09_2024/7x95_33067_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x95_33067/09_2024/7x95_33067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x95_33067/09_2024/7x95_33067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x95_33067/09_2024/7x95_33067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x95_33067/09_2024/7x95_33067_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x95_33067/09_2024/7x95_33067_trim.cif" } resolution = 3.9 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= 0.000 sd= 0.002 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 15 5.16 5 C 2137 2.51 5 N 557 2.21 5 O 637 1.98 5 H 3176 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6522 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3043 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "H" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1887 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1564 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.58, per 1000 atoms: 0.55 Number of scatterers: 6522 At special positions: 0 Unit cell: (90.361, 87.874, 66.32, 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 15 16.00 O 637 8.00 N 557 7.00 C 2137 6.00 H 3176 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 624.1 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 9.8% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.591A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.089A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.787A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.409A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.007A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.203A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.500A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.629A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'L' and resid 46 through 49 removed outlier: 5.563A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 228 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: 2.10 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3176 1.03 - 1.23: 10 1.23 - 1.42: 1526 1.42 - 1.62: 1883 1.62 - 1.81: 18 Bond restraints: 6613 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C3 NAG B 2 " pdb=" O3 NAG B 2 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C3 NAG B 1 " pdb=" O3 NAG B 1 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.78e-01 ... (remaining 6608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 11207 1.07 - 2.13: 592 2.13 - 3.20: 33 3.20 - 4.26: 11 4.26 - 5.33: 1 Bond angle restraints: 11844 Sorted by residual: angle pdb=" C LEU A 518 " pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " ideal model delta sigma weight residual 116.54 112.37 4.17 1.15e+00 7.56e-01 1.31e+01 angle pdb=" N GLY L 15 " pdb=" CA GLY L 15 " pdb=" C GLY L 15 " ideal model delta sigma weight residual 113.18 118.51 -5.33 2.37e+00 1.78e-01 5.06e+00 angle pdb=" CA GLY H 8 " pdb=" C GLY H 8 " pdb=" N GLY H 9 " ideal model delta sigma weight residual 114.85 116.83 -1.98 9.50e-01 1.11e+00 4.32e+00 angle pdb=" CA GLY H 8 " pdb=" C GLY H 8 " pdb=" O GLY H 8 " ideal model delta sigma weight residual 122.25 120.57 1.68 9.90e-01 1.02e+00 2.87e+00 angle pdb=" CA LEU A 518 " pdb=" C LEU A 518 " pdb=" N HIS A 519 " ideal model delta sigma weight residual 119.52 118.19 1.33 7.90e-01 1.60e+00 2.85e+00 ... (remaining 11839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 2909 17.50 - 35.00: 216 35.00 - 52.50: 80 52.50 - 70.00: 16 70.00 - 87.50: 2 Dihedral angle restraints: 3223 sinusoidal: 1702 harmonic: 1521 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 134.50 -41.50 1 1.00e+01 1.00e-02 2.41e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 56.62 36.38 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA LEU L 96 " pdb=" C LEU L 96 " pdb=" N PHE L 97 " pdb=" CA PHE L 97 " ideal model delta harmonic sigma weight residual 180.00 -161.73 -18.27 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 3220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 275 0.026 - 0.053: 153 0.053 - 0.079: 38 0.079 - 0.106: 23 0.106 - 0.132: 16 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL L 59 " pdb=" N VAL L 59 " pdb=" C VAL L 59 " pdb=" CB VAL L 59 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL H 122 " pdb=" N VAL H 122 " pdb=" C VAL H 122 " pdb=" CB VAL H 122 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 502 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 13 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO L 14 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO L 8 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO A 463 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.014 5.00e-02 4.00e+02 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 508 2.20 - 2.80: 13089 2.80 - 3.40: 16606 3.40 - 4.00: 22671 4.00 - 4.60: 33900 Nonbonded interactions: 86774 Sorted by model distance: nonbonded pdb=" H GLN H 100 " pdb=" OD2 ASP H 114 " model vdw 1.601 2.450 nonbonded pdb=" O PHE H 29 " pdb="HH22 ARG H 72 " model vdw 1.623 2.450 nonbonded pdb="HH22 ARG H 67 " pdb=" OD2 ASP H 90 " model vdw 1.636 2.450 nonbonded pdb=" OD1 ASP L 86 " pdb=" H THR L 104 " model vdw 1.647 2.450 nonbonded pdb=" HZ2 LYS A 417 " pdb=" OH TYR H 109 " model vdw 1.681 2.450 ... (remaining 86769 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 group one per residue 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: 0.220 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: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.930 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.003 0.035 3437 Z= 0.167 Angle : 0.503 5.329 4676 Z= 0.267 Chirality : 0.042 0.132 505 Planarity : 0.004 0.060 598 Dihedral : 13.803 87.503 1235 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.00 (0.42), residues: 421 helix: -1.95 (1.84), residues: 12 sheet: 0.33 (0.45), residues: 137 loop : -1.18 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 36 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE A 400 TYR 0.012 0.001 TYR A 453 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8532 (p0) cc_final: 0.8309 (p0) REVERT: H 35 HIS cc_start: 0.6588 (m170) cc_final: 0.6326 (m-70) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.4133 time to fit residues: 39.9027 Evaluate side-chains 52 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 0.0870 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3437 Z= 0.232 Angle : 0.557 5.120 4676 Z= 0.289 Chirality : 0.041 0.134 505 Planarity : 0.004 0.063 598 Dihedral : 6.766 56.020 514 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.11 % Allowed : 8.36 % Favored : 90.53 % 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: -1.10 (0.41), residues: 421 helix: -1.84 (1.89), residues: 12 sheet: 0.19 (0.45), residues: 138 loop : -1.23 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 98 HIS 0.001 0.000 HIS L 39 PHE 0.005 0.001 PHE A 400 TYR 0.007 0.001 TYR A 453 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 HIS cc_start: 0.6324 (m170) cc_final: 0.5224 (m170) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.3424 time to fit residues: 26.1918 Evaluate side-chains 54 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3437 Z= 0.291 Angle : 0.576 4.981 4676 Z= 0.300 Chirality : 0.041 0.142 505 Planarity : 0.004 0.065 598 Dihedral : 6.369 45.525 514 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.56 % Allowed : 10.58 % Favored : 88.86 % 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: -1.14 (0.41), residues: 421 helix: -1.60 (1.99), residues: 12 sheet: 0.10 (0.45), residues: 136 loop : -1.22 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.005 0.002 HIS H 35 PHE 0.009 0.001 PHE A 456 TYR 0.006 0.001 TYR A 453 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.3584 time to fit residues: 24.4979 Evaluate side-chains 53 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.7722 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3437 Z= 0.250 Angle : 0.558 5.096 4676 Z= 0.289 Chirality : 0.041 0.137 505 Planarity : 0.004 0.063 598 Dihedral : 5.747 44.252 514 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.56 % Allowed : 12.53 % Favored : 86.91 % 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: -1.07 (0.41), residues: 421 helix: -1.57 (1.97), residues: 12 sheet: 0.27 (0.47), residues: 133 loop : -1.23 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS L 39 PHE 0.009 0.001 PHE A 456 TYR 0.006 0.001 TYR H 108 ARG 0.001 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 53 average time/residue: 0.3718 time to fit residues: 24.2810 Evaluate side-chains 47 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN L 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3437 Z= 0.334 Angle : 0.603 5.435 4676 Z= 0.314 Chirality : 0.041 0.149 505 Planarity : 0.004 0.063 598 Dihedral : 5.654 44.736 514 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.84 % Allowed : 14.21 % Favored : 84.96 % 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: -1.21 (0.40), residues: 421 helix: -1.93 (1.77), residues: 12 sheet: 0.16 (0.45), residues: 133 loop : -1.31 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.003 0.001 HIS L 39 PHE 0.014 0.001 PHE H 107 TYR 0.009 0.001 TYR A 365 ARG 0.001 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 0.3203 time to fit residues: 20.3252 Evaluate side-chains 46 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 28 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3437 Z= 0.262 Angle : 0.584 6.726 4676 Z= 0.302 Chirality : 0.042 0.147 505 Planarity : 0.004 0.061 598 Dihedral : 5.512 43.798 514 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 16.71 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.20 (0.40), residues: 421 helix: -1.76 (1.82), residues: 12 sheet: 0.18 (0.44), residues: 133 loop : -1.31 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 36 HIS 0.001 0.001 HIS L 39 PHE 0.012 0.001 PHE L 97 TYR 0.006 0.001 TYR A 365 ARG 0.001 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3381 time to fit residues: 20.1369 Evaluate side-chains 46 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3437 Z= 0.314 Angle : 0.610 9.520 4676 Z= 0.315 Chirality : 0.041 0.145 505 Planarity : 0.004 0.061 598 Dihedral : 5.541 44.193 514 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.11 % Allowed : 15.88 % Favored : 83.01 % 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: -1.30 (0.39), residues: 421 helix: -2.29 (1.24), residues: 18 sheet: 0.24 (0.45), residues: 132 loop : -1.39 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.010 0.002 HIS L 39 PHE 0.009 0.001 PHE H 107 TYR 0.009 0.001 TYR A 365 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.3394 time to fit residues: 20.2976 Evaluate side-chains 49 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3437 Z= 0.231 Angle : 0.590 9.277 4676 Z= 0.304 Chirality : 0.042 0.145 505 Planarity : 0.004 0.061 598 Dihedral : 5.316 42.810 514 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.28 % Allowed : 16.99 % Favored : 82.73 % 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: -1.24 (0.39), residues: 421 helix: -2.20 (1.34), residues: 18 sheet: 0.23 (0.44), residues: 132 loop : -1.32 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.002 0.000 HIS L 39 PHE 0.010 0.001 PHE L 97 TYR 0.005 0.001 TYR A 365 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 54 average time/residue: 0.3453 time to fit residues: 22.5103 Evaluate side-chains 52 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3437 Z= 0.246 Angle : 0.589 9.365 4676 Z= 0.302 Chirality : 0.041 0.142 505 Planarity : 0.004 0.061 598 Dihedral : 5.202 42.628 514 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.84 % Allowed : 16.99 % Favored : 82.17 % 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: -1.30 (0.39), residues: 421 helix: -2.50 (1.27), residues: 18 sheet: 0.11 (0.44), residues: 134 loop : -1.32 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.002 0.001 HIS L 39 PHE 0.011 0.001 PHE L 97 TYR 0.005 0.001 TYR A 365 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 52 average time/residue: 0.3369 time to fit residues: 21.4783 Evaluate side-chains 51 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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: 0.7843 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3437 Z= 0.266 Angle : 0.604 9.598 4676 Z= 0.313 Chirality : 0.041 0.138 505 Planarity : 0.004 0.061 598 Dihedral : 5.327 42.299 514 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.56 % Allowed : 17.55 % Favored : 81.89 % 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: -1.37 (0.39), residues: 421 helix: -2.81 (1.23), residues: 18 sheet: 0.04 (0.44), residues: 134 loop : -1.32 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.002 0.001 HIS L 39 PHE 0.011 0.001 PHE A 456 TYR 0.008 0.001 TYR A 489 ARG 0.002 0.000 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.3597 time to fit residues: 21.7950 Evaluate side-chains 51 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 = 0.2881 r_free = 0.2881 target = 0.041393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.033535 restraints weight = 55904.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.035622 restraints weight = 21356.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.037079 restraints weight = 11084.939| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3437 Z= 0.219 Angle : 0.586 9.446 4676 Z= 0.302 Chirality : 0.041 0.137 505 Planarity : 0.004 0.061 598 Dihedral : 5.077 40.429 514 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 18.11 % Favored : 81.89 % 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: -1.29 (0.40), residues: 421 helix: -2.82 (1.29), residues: 18 sheet: 0.04 (0.44), residues: 134 loop : -1.23 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 116 HIS 0.001 0.001 HIS L 39 PHE 0.013 0.001 PHE A 456 TYR 0.005 0.001 TYR A 453 ARG 0.003 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2127.51 seconds wall clock time: 37 minutes 40.56 seconds (2260.56 seconds total)