Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:55:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/11_2022/7v48_31703.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/11_2022/7v48_31703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/11_2022/7v48_31703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/11_2022/7v48_31703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/11_2022/7v48_31703.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v48_31703/11_2022/7v48_31703.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 98": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2598 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "A" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Time building chain proxies: 2.00, per 1000 atoms: 0.77 Number of scatterers: 2598 At special positions: 0 Unit cell: (104.94, 110.24, 32.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 522 8.00 N 450 7.00 C 1626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 733.7 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 38 through 40 removed outlier: 6.719A pdb=" N TYR B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.501A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'E' and resid 75 through 79 removed outlier: 6.608A pdb=" N ALA B 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLN F 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 82 through 83 removed outlier: 6.541A pdb=" N VAL B 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.748A pdb=" N TYR A 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.513A pdb=" N VAL A 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 79 removed outlier: 6.603A pdb=" N ALA A 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLN D 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA A 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.549A pdb=" N VAL A 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) 19 hydrogen bonds defined for protein. 57 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: 0.54 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 456 1.29 - 1.36: 408 1.36 - 1.42: 102 1.42 - 1.49: 426 1.49 - 1.55: 1218 Bond restraints: 2610 Sorted by residual: bond pdb=" CA ALA D 90 " pdb=" C ALA D 90 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.10e-02 8.26e+03 4.74e-01 bond pdb=" CA ALA F 90 " pdb=" C ALA F 90 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.10e-02 8.26e+03 4.74e-01 bond pdb=" CA ALA A 90 " pdb=" C ALA A 90 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.10e-02 8.26e+03 4.70e-01 bond pdb=" CA ALA B 90 " pdb=" C ALA B 90 " ideal model delta sigma weight residual 1.530 1.523 0.007 1.10e-02 8.26e+03 4.14e-01 bond pdb=" CA ALA E 90 " pdb=" C ALA E 90 " ideal model delta sigma weight residual 1.530 1.523 0.007 1.10e-02 8.26e+03 4.09e-01 ... (remaining 2605 not shown) Histogram of bond angle deviations from ideal: 105.88 - 110.97: 1036 110.97 - 116.06: 862 116.06 - 121.15: 767 121.15 - 126.24: 857 126.24 - 131.32: 6 Bond angle restraints: 3528 Sorted by residual: angle pdb=" CA ALA F 90 " pdb=" C ALA F 90 " pdb=" N ALA F 91 " ideal model delta sigma weight residual 114.76 116.75 -1.99 1.14e+00 7.69e-01 3.05e+00 angle pdb=" CA ALA D 90 " pdb=" C ALA D 90 " pdb=" N ALA D 91 " ideal model delta sigma weight residual 114.76 116.71 -1.95 1.14e+00 7.69e-01 2.94e+00 angle pdb=" CA ALA C 90 " pdb=" C ALA C 90 " pdb=" N ALA C 91 " ideal model delta sigma weight residual 114.76 116.69 -1.93 1.14e+00 7.69e-01 2.86e+00 angle pdb=" CA ALA A 90 " pdb=" C ALA A 90 " pdb=" N ALA A 91 " ideal model delta sigma weight residual 114.76 116.69 -1.93 1.14e+00 7.69e-01 2.86e+00 angle pdb=" CA ALA E 90 " pdb=" C ALA E 90 " pdb=" N ALA E 91 " ideal model delta sigma weight residual 114.76 116.68 -1.92 1.14e+00 7.69e-01 2.84e+00 ... (remaining 3523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.21: 1350 13.21 - 26.41: 120 26.41 - 39.62: 36 39.62 - 52.82: 0 52.82 - 66.03: 12 Dihedral angle restraints: 1518 sinusoidal: 504 harmonic: 1014 Sorted by residual: dihedral pdb=" CA ASP B 98 " pdb=" CB ASP B 98 " pdb=" CG ASP B 98 " pdb=" OD1 ASP B 98 " ideal model delta sinusoidal sigma weight residual -30.00 -89.45 59.45 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP F 98 " pdb=" CB ASP F 98 " pdb=" CG ASP F 98 " pdb=" OD1 ASP F 98 " ideal model delta sinusoidal sigma weight residual -30.00 -89.44 59.44 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP C 98 " pdb=" CB ASP C 98 " pdb=" CG ASP C 98 " pdb=" OD1 ASP C 98 " ideal model delta sinusoidal sigma weight residual -30.00 -89.41 59.41 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 1515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 227 0.026 - 0.053: 128 0.053 - 0.079: 35 0.079 - 0.106: 37 0.106 - 0.132: 35 Chirality restraints: 462 Sorted by residual: chirality pdb=" CA VAL C 66 " pdb=" N VAL C 66 " pdb=" C VAL C 66 " pdb=" CB VAL C 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL D 66 " pdb=" N VAL D 66 " pdb=" C VAL D 66 " pdb=" CB VAL D 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL F 66 " pdb=" N VAL F 66 " pdb=" C VAL F 66 " pdb=" CB VAL F 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 459 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 68 " 0.003 2.00e-02 2.50e+03 6.10e-03 3.72e-01 pdb=" C GLY B 68 " -0.011 2.00e-02 2.50e+03 pdb=" O GLY B 68 " 0.004 2.00e-02 2.50e+03 pdb=" N ALA B 69 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 68 " -0.003 2.00e-02 2.50e+03 6.08e-03 3.70e-01 pdb=" C GLY A 68 " 0.011 2.00e-02 2.50e+03 pdb=" O GLY A 68 " -0.004 2.00e-02 2.50e+03 pdb=" N ALA A 69 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 68 " -0.003 2.00e-02 2.50e+03 6.04e-03 3.65e-01 pdb=" C GLY D 68 " 0.010 2.00e-02 2.50e+03 pdb=" O GLY D 68 " -0.004 2.00e-02 2.50e+03 pdb=" N ALA D 69 " -0.004 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 716 2.82 - 3.34: 2357 3.34 - 3.86: 3650 3.86 - 4.38: 4096 4.38 - 4.90: 8597 Nonbonded interactions: 19416 Sorted by model distance: nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.295 2.520 nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.296 2.520 nonbonded pdb=" NE2 GLN F 62 " pdb=" OG1 THR F 64 " model vdw 2.296 2.520 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.296 2.520 nonbonded pdb=" NE2 GLN D 62 " pdb=" OG1 THR D 64 " model vdw 2.296 2.520 ... (remaining 19411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1626 2.51 5 N 450 2.21 5 O 522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.720 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 13.250 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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 : 0.002 0.009 2610 Z= 0.120 Angle : 0.484 2.756 3528 Z= 0.293 Chirality : 0.051 0.132 462 Planarity : 0.001 0.006 438 Dihedral : 12.912 66.027 882 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 0.00 % 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: -5.61 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.22), residues: 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.295 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.8521 time to fit residues: 58.9710 Evaluate side-chains 47 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.296 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN E 62 GLN E 79 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN D 62 GLN D 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 2610 Z= 0.301 Angle : 0.559 3.694 3528 Z= 0.317 Chirality : 0.050 0.125 462 Planarity : 0.003 0.009 438 Dihedral : 4.907 14.460 378 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.68 % Favored : 77.32 % Rotamer Outliers : 6.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.23), residues: 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 0.291 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 64 average time/residue: 0.7329 time to fit residues: 48.4193 Evaluate side-chains 52 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.230 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.0243 time to fit residues: 0.4324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.032 2610 Z= 0.415 Angle : 0.658 5.030 3528 Z= 0.375 Chirality : 0.052 0.126 462 Planarity : 0.004 0.011 438 Dihedral : 5.475 14.217 378 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.23 % Favored : 73.77 % Rotamer Outliers : 6.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.46 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.23), residues: 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.301 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 54 average time/residue: 0.8596 time to fit residues: 47.9505 Evaluate side-chains 53 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.0267 time to fit residues: 0.6357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 0.0020 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 2610 Z= 0.133 Angle : 0.460 3.402 3528 Z= 0.254 Chirality : 0.050 0.130 462 Planarity : 0.001 0.010 438 Dihedral : 4.280 12.593 378 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer Outliers : 6.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.80 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.25), residues: 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.306 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 58 average time/residue: 0.8229 time to fit residues: 49.3449 Evaluate side-chains 48 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0274 time to fit residues: 0.4773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 0.0270 overall best weight: 3.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 2610 Z= 0.296 Angle : 0.559 5.639 3528 Z= 0.315 Chirality : 0.050 0.125 462 Planarity : 0.003 0.017 438 Dihedral : 4.730 14.716 378 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.77 % Favored : 76.23 % Rotamer Outliers : 4.92 % 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: -4.98 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.25), residues: 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.320 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 55 average time/residue: 0.7862 time to fit residues: 44.7434 Evaluate side-chains 51 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.266 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0260 time to fit residues: 0.3898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 2610 Z= 0.170 Angle : 0.498 5.935 3528 Z= 0.275 Chirality : 0.050 0.127 462 Planarity : 0.002 0.019 438 Dihedral : 4.283 13.305 378 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer Outliers : 5.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.26), residues: 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.298 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 57 average time/residue: 0.7729 time to fit residues: 45.5859 Evaluate side-chains 50 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0260 time to fit residues: 0.4186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 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: 0.7522 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.029 2610 Z= 0.357 Angle : 0.623 6.598 3528 Z= 0.351 Chirality : 0.050 0.121 462 Planarity : 0.003 0.019 438 Dihedral : 4.983 15.619 378 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.41 % Favored : 74.59 % Rotamer Outliers : 4.55 % 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: -5.02 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.24), residues: 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.305 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 50 average time/residue: 0.8502 time to fit residues: 44.1831 Evaluate side-chains 51 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.0309 time to fit residues: 0.5195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.7487 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 2610 Z= 0.255 Angle : 0.562 6.132 3528 Z= 0.312 Chirality : 0.050 0.126 462 Planarity : 0.003 0.020 438 Dihedral : 4.751 14.857 378 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.03 % Favored : 81.97 % Rotamer Outliers : 4.55 % 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: -4.88 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.25), residues: 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.285 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 53 average time/residue: 0.8599 time to fit residues: 47.0992 Evaluate side-chains 51 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.299 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0268 time to fit residues: 0.4483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.7457 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2610 Z= 0.198 Angle : 0.537 6.994 3528 Z= 0.295 Chirality : 0.050 0.137 462 Planarity : 0.002 0.021 438 Dihedral : 4.395 13.790 378 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.03 % Favored : 81.97 % Rotamer Outliers : 4.55 % 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: -4.70 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.26), residues: 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.306 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 55 average time/residue: 0.8810 time to fit residues: 50.1318 Evaluate side-chains 52 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.293 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0365 time to fit residues: 0.4597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.3980 chunk 22 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.031 2610 Z= 0.385 Angle : 0.673 7.407 3528 Z= 0.376 Chirality : 0.051 0.125 462 Planarity : 0.004 0.022 438 Dihedral : 5.188 15.673 378 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.68 % Favored : 74.32 % Rotamer Outliers : 4.55 % 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: -5.16 (0.31), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.24), residues: 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.306 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 52 average time/residue: 0.8561 time to fit residues: 46.0227 Evaluate side-chains 51 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0257 time to fit residues: 0.4706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 = 0.4538 r_free = 0.4538 target = 0.164495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.121747 restraints weight = 2892.255| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.90 r_work: 0.4002 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work: 0.3974 rms_B_bonded: 2.64 restraints_weight: 0.1250 r_work: 0.3958 rms_B_bonded: 2.76 restraints_weight: 0.0625 r_work: 0.3940 rms_B_bonded: 2.93 restraints_weight: 0.0312 r_work: 0.3920 rms_B_bonded: 3.15 restraints_weight: 0.0156 r_work: 0.3898 rms_B_bonded: 3.44 restraints_weight: 0.0078 r_work: 0.3873 rms_B_bonded: 3.81 restraints_weight: 0.0039 r_work: 0.3845 rms_B_bonded: 4.25 restraints_weight: 0.0020 r_work: 0.3814 rms_B_bonded: 4.80 restraints_weight: 0.0010 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 2610 Z= 0.222 Angle : 0.563 7.137 3528 Z= 0.309 Chirality : 0.050 0.125 462 Planarity : 0.002 0.021 438 Dihedral : 4.665 14.475 378 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.94 % Favored : 83.06 % Rotamer Outliers : 3.03 % 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: -4.88 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.25), residues: 366 =============================================================================== Job complete usr+sys time: 1378.47 seconds wall clock time: 25 minutes 14.07 seconds (1514.07 seconds total)