Starting phenix.real_space_refine on Fri Aug 2 15:18:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khd_37241/08_2024/8khd_37241.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khd_37241/08_2024/8khd_37241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khd_37241/08_2024/8khd_37241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khd_37241/08_2024/8khd_37241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khd_37241/08_2024/8khd_37241.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khd_37241/08_2024/8khd_37241.cif" } resolution = 3.5 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= 0.057 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 17 5.16 5 C 2112 2.51 5 N 561 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3337 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 917 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "C" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1600 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" 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: 3.16, per 1000 atoms: 0.95 Number of scatterers: 3337 At special positions: 0 Unit cell: (69.96, 90.1, 86.92, 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 17 16.00 O 647 8.00 N 561 7.00 C 2112 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 98 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 87 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 C 601 " - " ASN C 343 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 658.8 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 7 sheets defined 3.5% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.696A pdb=" N ASP H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 408 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 45 through 50 removed outlier: 6.501A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 104 through 106 removed outlier: 4.357A pdb=" N VAL H 105 " --> pdb=" O ARG C 466 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 466 " --> pdb=" O VAL H 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'J' and resid 9 through 10 removed outlier: 6.699A pdb=" N TRP J 34 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.600A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 85 hydrogen bonds defined for protein. 219 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: 0.75 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1087 1.35 - 1.48: 932 1.48 - 1.61: 1377 1.61 - 1.74: 0 1.74 - 1.87: 22 Bond restraints: 3418 Sorted by residual: bond pdb=" CG1 ILE C 434 " pdb=" CD1 ILE C 434 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.67e+00 bond pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 1.808 1.865 -0.057 3.30e-02 9.18e+02 3.00e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" CA ASN C 331 " pdb=" C ASN C 331 " ideal model delta sigma weight residual 1.521 1.537 -0.016 9.90e-03 1.02e+04 2.67e+00 bond pdb=" C ASN C 331 " pdb=" N ILE C 332 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.40e-02 5.10e+03 2.18e+00 ... (remaining 3413 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.10: 103 107.10 - 113.83: 1798 113.83 - 120.55: 1283 120.55 - 127.27: 1427 127.27 - 134.00: 39 Bond angle restraints: 4650 Sorted by residual: angle pdb=" C ASN C 331 " pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 121.70 129.97 -8.27 1.80e+00 3.09e-01 2.11e+01 angle pdb=" C VAL J 97 " pdb=" N ILE J 98 " pdb=" CA ILE J 98 " ideal model delta sigma weight residual 121.97 129.47 -7.50 1.80e+00 3.09e-01 1.73e+01 angle pdb=" CB MET H 122 " pdb=" CG MET H 122 " pdb=" SD MET H 122 " ideal model delta sigma weight residual 112.70 124.35 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CA CYS C 379 " pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " ideal model delta sigma weight residual 114.40 123.01 -8.61 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA TYR H 109 " pdb=" CB TYR H 109 " pdb=" CG TYR H 109 " ideal model delta sigma weight residual 113.90 120.63 -6.73 1.80e+00 3.09e-01 1.40e+01 ... (remaining 4645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 1834 17.62 - 35.25: 158 35.25 - 52.87: 23 52.87 - 70.49: 5 70.49 - 88.11: 2 Dihedral angle restraints: 2022 sinusoidal: 781 harmonic: 1241 Sorted by residual: dihedral pdb=" CA ALA C 372 " pdb=" C ALA C 372 " pdb=" N PRO C 373 " pdb=" CA PRO C 373 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA CYS C 379 " pdb=" C CYS C 379 " pdb=" N TYR C 380 " pdb=" CA TYR C 380 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 58.41 34.59 1 1.00e+01 1.00e-02 1.70e+01 ... (remaining 2019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 355 0.045 - 0.089: 103 0.089 - 0.134: 47 0.134 - 0.178: 1 0.178 - 0.223: 3 Chirality restraints: 509 Sorted by residual: chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB THR H 59 " pdb=" CA THR H 59 " pdb=" OG1 THR H 59 " pdb=" CG2 THR H 59 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA CYS C 379 " pdb=" N CYS C 379 " pdb=" C CYS C 379 " pdb=" CB CYS C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 506 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 374 " 0.015 2.00e-02 2.50e+03 1.66e-02 4.82e+00 pdb=" CG PHE C 374 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE C 374 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 374 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 374 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 374 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 374 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET H 108 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C MET H 108 " 0.037 2.00e-02 2.50e+03 pdb=" O MET H 108 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR H 109 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP J 7 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO J 8 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO J 8 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 8 " 0.028 5.00e-02 4.00e+02 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 952 2.81 - 3.33: 2787 3.33 - 3.85: 5267 3.85 - 4.38: 5755 4.38 - 4.90: 10283 Nonbonded interactions: 25044 Sorted by model distance: nonbonded pdb=" OG SER J 64 " pdb=" OG SER J 71 " model vdw 2.287 3.040 nonbonded pdb=" OG SER J 66 " pdb=" OG1 THR J 69 " model vdw 2.302 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.313 3.040 nonbonded pdb=" O VAL J 97 " pdb=" N PHE J 99 " model vdw 2.354 3.120 nonbonded pdb=" O ILE H 55 " pdb=" ND2 ASN C 354 " model vdw 2.355 3.120 ... (remaining 25039 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.850 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 3418 Z= 0.271 Angle : 0.876 11.654 4650 Z= 0.464 Chirality : 0.050 0.223 509 Planarity : 0.006 0.051 604 Dihedral : 13.417 88.113 1218 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.28 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.39 (0.41), residues: 426 helix: -4.55 (0.52), residues: 13 sheet: 0.98 (0.49), residues: 122 loop : -1.74 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 353 HIS 0.002 0.001 HIS J 96 PHE 0.039 0.002 PHE C 374 TYR 0.034 0.002 TYR C 369 ARG 0.006 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1861 time to fit residues: 17.4606 Evaluate side-chains 64 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN C 394 ASN C 474 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3418 Z= 0.273 Angle : 0.657 7.968 4650 Z= 0.345 Chirality : 0.044 0.182 509 Planarity : 0.005 0.041 604 Dihedral : 5.749 30.123 496 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.75 % Favored : 92.02 % Rotamer: Outliers : 3.36 % Allowed : 11.76 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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 (0.41), residues: 426 helix: -4.36 (0.66), residues: 19 sheet: 1.13 (0.48), residues: 123 loop : -1.66 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS C 505 PHE 0.012 0.001 PHE C 400 TYR 0.012 0.002 TYR C 369 ARG 0.003 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.370 Fit side-chains REVERT: H 107 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6433 (ptp) REVERT: C 360 ASN cc_start: 0.8400 (m-40) cc_final: 0.8182 (m-40) REVERT: C 390 LEU cc_start: 0.7108 (pt) cc_final: 0.6777 (tt) outliers start: 12 outliers final: 7 residues processed: 72 average time/residue: 0.1479 time to fit residues: 13.1264 Evaluate side-chains 65 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3418 Z= 0.187 Angle : 0.603 8.114 4650 Z= 0.310 Chirality : 0.043 0.169 509 Planarity : 0.004 0.040 604 Dihedral : 5.288 27.566 496 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.69 % Favored : 91.08 % Rotamer: Outliers : 2.24 % Allowed : 17.65 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.19 (0.41), residues: 426 helix: -3.96 (0.83), residues: 18 sheet: 1.28 (0.49), residues: 119 loop : -1.61 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.009 0.001 PHE C 338 TYR 0.013 0.001 TYR C 380 ARG 0.002 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: H 92 ASP cc_start: 0.7893 (m-30) cc_final: 0.7640 (m-30) REVERT: H 107 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.6154 (ptp) REVERT: C 390 LEU cc_start: 0.7005 (pt) cc_final: 0.6633 (tt) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 0.1341 time to fit residues: 11.7215 Evaluate side-chains 64 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7204 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3418 Z= 0.196 Angle : 0.603 8.114 4650 Z= 0.311 Chirality : 0.043 0.169 509 Planarity : 0.004 0.038 604 Dihedral : 5.141 26.430 496 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.98 % Favored : 91.78 % Rotamer: Outliers : 2.52 % Allowed : 17.93 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.03 (0.42), residues: 426 helix: -3.60 (1.19), residues: 13 sheet: 1.25 (0.48), residues: 119 loop : -1.50 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.016 0.001 PHE C 338 TYR 0.017 0.001 TYR C 369 ARG 0.004 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.392 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 75 average time/residue: 0.1299 time to fit residues: 12.3500 Evaluate side-chains 70 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 36 GLN ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3418 Z= 0.195 Angle : 0.614 8.457 4650 Z= 0.315 Chirality : 0.043 0.166 509 Planarity : 0.004 0.036 604 Dihedral : 5.183 25.588 496 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.62 % Favored : 90.14 % Rotamer: Outliers : 3.36 % Allowed : 17.65 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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 (0.42), residues: 426 helix: -3.88 (0.83), residues: 18 sheet: 0.98 (0.48), residues: 125 loop : -1.46 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.009 0.001 PHE C 338 TYR 0.012 0.001 TYR C 369 ARG 0.002 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: H 92 ASP cc_start: 0.7900 (m-30) cc_final: 0.7690 (m-30) REVERT: C 390 LEU cc_start: 0.6970 (pt) cc_final: 0.6557 (tt) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.1267 time to fit residues: 12.4108 Evaluate side-chains 73 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.0170 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 36 GLN ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3418 Z= 0.200 Angle : 0.608 7.721 4650 Z= 0.313 Chirality : 0.044 0.164 509 Planarity : 0.004 0.036 604 Dihedral : 5.188 25.154 496 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.69 % Favored : 91.08 % Rotamer: Outliers : 3.64 % Allowed : 17.65 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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 (0.42), residues: 426 helix: -3.94 (0.76), residues: 19 sheet: 1.19 (0.49), residues: 120 loop : -1.46 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.008 0.001 PHE C 338 TYR 0.012 0.001 TYR C 380 ARG 0.002 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: H 119 GLN cc_start: 0.7485 (pp30) cc_final: 0.7239 (pp30) REVERT: J 104 LYS cc_start: 0.7102 (ttmm) cc_final: 0.6326 (tmtt) REVERT: C 390 LEU cc_start: 0.7191 (pt) cc_final: 0.6833 (tt) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.1390 time to fit residues: 13.8155 Evaluate side-chains 76 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3418 Z= 0.216 Angle : 0.616 8.877 4650 Z= 0.317 Chirality : 0.044 0.164 509 Planarity : 0.004 0.036 604 Dihedral : 5.257 25.512 496 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.92 % Favored : 90.85 % Rotamer: Outliers : 4.20 % Allowed : 18.49 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -1.02 (0.42), residues: 426 helix: -3.65 (0.83), residues: 18 sheet: 1.19 (0.48), residues: 119 loop : -1.39 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.009 0.001 PHE C 374 TYR 0.011 0.001 TYR J 48 ARG 0.003 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: J 104 LYS cc_start: 0.7111 (ttmm) cc_final: 0.6322 (tmtt) REVERT: C 390 LEU cc_start: 0.7048 (pt) cc_final: 0.6679 (tt) outliers start: 15 outliers final: 13 residues processed: 80 average time/residue: 0.1224 time to fit residues: 12.4751 Evaluate side-chains 80 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3418 Z= 0.174 Angle : 0.627 8.553 4650 Z= 0.320 Chirality : 0.044 0.160 509 Planarity : 0.004 0.036 604 Dihedral : 5.064 23.947 496 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.22 % Favored : 91.55 % Rotamer: Outliers : 3.08 % Allowed : 20.45 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -0.90 (0.43), residues: 426 helix: -3.40 (0.95), residues: 18 sheet: 1.24 (0.49), residues: 118 loop : -1.30 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS J 96 PHE 0.007 0.001 PHE C 338 TYR 0.012 0.001 TYR C 380 ARG 0.003 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: J 104 LYS cc_start: 0.7071 (ttmm) cc_final: 0.6313 (tmtt) REVERT: C 357 ARG cc_start: 0.7741 (tmm-80) cc_final: 0.7444 (ttm-80) REVERT: C 390 LEU cc_start: 0.7026 (pt) cc_final: 0.6659 (tt) outliers start: 11 outliers final: 9 residues processed: 76 average time/residue: 0.1457 time to fit residues: 13.7049 Evaluate side-chains 74 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.0070 chunk 39 optimal weight: 0.0670 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 36 GLN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3418 Z= 0.291 Angle : 0.699 8.232 4650 Z= 0.362 Chirality : 0.045 0.165 509 Planarity : 0.005 0.037 604 Dihedral : 5.627 26.774 496 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.27 % Favored : 88.50 % Rotamer: Outliers : 4.20 % Allowed : 21.57 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.42), residues: 426 helix: -3.56 (0.90), residues: 19 sheet: 0.97 (0.48), residues: 119 loop : -1.46 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS J 96 PHE 0.011 0.001 PHE H 82 TYR 0.014 0.002 TYR C 369 ARG 0.003 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: J 104 LYS cc_start: 0.7178 (ttmm) cc_final: 0.6346 (tmtt) outliers start: 15 outliers final: 11 residues processed: 78 average time/residue: 0.1450 time to fit residues: 14.0892 Evaluate side-chains 78 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.0370 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.0060 overall best weight: 0.4474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3418 Z= 0.178 Angle : 0.676 9.048 4650 Z= 0.345 Chirality : 0.044 0.160 509 Planarity : 0.004 0.035 604 Dihedral : 5.153 23.111 496 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.28 % Favored : 92.49 % Rotamer: Outliers : 2.24 % Allowed : 23.53 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -0.93 (0.43), residues: 426 helix: -3.26 (1.03), residues: 18 sheet: 1.00 (0.48), residues: 122 loop : -1.25 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS J 96 PHE 0.009 0.001 PHE H 82 TYR 0.015 0.001 TYR C 380 ARG 0.003 0.000 ARG J 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: J 104 LYS cc_start: 0.7076 (ttmm) cc_final: 0.6312 (tmtt) outliers start: 8 outliers final: 7 residues processed: 72 average time/residue: 0.1627 time to fit residues: 14.3172 Evaluate side-chains 71 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.150886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.121654 restraints weight = 6233.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.126550 restraints weight = 3347.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.129792 restraints weight = 2338.585| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3418 Z= 0.180 Angle : 0.663 9.091 4650 Z= 0.336 Chirality : 0.044 0.159 509 Planarity : 0.004 0.035 604 Dihedral : 5.074 22.815 496 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.45 % Favored : 91.31 % Rotamer: Outliers : 1.96 % Allowed : 23.81 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -0.90 (0.42), residues: 426 helix: -2.38 (1.46), residues: 12 sheet: 0.70 (0.45), residues: 130 loop : -1.22 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.001 HIS J 96 PHE 0.010 0.001 PHE H 82 TYR 0.017 0.001 TYR C 369 ARG 0.002 0.000 ARG C 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1283.57 seconds wall clock time: 23 minutes 45.77 seconds (1425.77 seconds total)