Starting phenix.real_space_refine (version: dev) on Mon Feb 20 11:36:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/02_2023/7wkw_32570_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/02_2023/7wkw_32570.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/02_2023/7wkw_32570_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/02_2023/7wkw_32570_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/02_2023/7wkw_32570_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/02_2023/7wkw_32570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/02_2023/7wkw_32570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/02_2023/7wkw_32570_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/02_2023/7wkw_32570_trim_updated.pdb" } resolution = 2.62 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= 0.005 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12056 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6006 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "A" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6006 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'E7O': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'E7O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.29, per 1000 atoms: 0.52 Number of scatterers: 12056 At special positions: 0 Unit cell: (80.845, 121.693, 71.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 O 998 8.00 N 940 7.00 C 3938 6.00 H 6138 1.00 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: 10.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 2 sheets defined 72.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'B' and resid 4 through 29 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 36 through 59 removed outlier: 4.807A pdb=" N VAL B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.760A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 144 through 164 Processing helix chain 'B' and resid 476 through 491 Processing helix chain 'B' and resid 495 through 513 Processing helix chain 'B' and resid 519 through 546 removed outlier: 4.214A pdb=" N LEU B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU B 533 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY B 534 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 580 removed outlier: 4.262A pdb=" N GLY B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) Proline residue: B 570 - end of helix Processing helix chain 'B' and resid 584 through 594 removed outlier: 4.004A pdb=" N ARG B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 Processing helix chain 'B' and resid 613 through 639 removed outlier: 4.738A pdb=" N LEU B 628 " --> pdb=" O MET B 624 " (cutoff:3.500A) Proline residue: B 629 - end of helix Processing helix chain 'A' and resid 4 through 29 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 36 through 59 removed outlier: 4.811A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.764A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 144 through 164 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 476 through 491 Processing helix chain 'A' and resid 495 through 513 Processing helix chain 'A' and resid 519 through 546 removed outlier: 4.208A pdb=" N LEU A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU A 533 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 580 removed outlier: 4.262A pdb=" N GLY A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 584 through 594 removed outlier: 3.978A pdb=" N ARG A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 Processing helix chain 'A' and resid 613 through 639 removed outlier: 4.727A pdb=" N LEU A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 174 through 177 removed outlier: 4.267A pdb=" N SER B 174 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 174 through 177 removed outlier: 4.270A pdb=" N SER A 174 " --> pdb=" O LEU A 202 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1206 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: 3.85 Time building geometry restraints manager: 10.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 6132 1.02 - 1.21: 8 1.21 - 1.41: 2426 1.41 - 1.61: 3560 1.61 - 1.81: 78 Bond restraints: 12204 Sorted by residual: bond pdb=" ND2 ASN A 112 " pdb="HD22 ASN A 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN A 112 " pdb="HD21 ASN A 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN B 112 " pdb="HD21 ASN B 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN B 112 " pdb="HD22 ASN B 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA TYR B 145 " pdb=" C TYR B 145 " ideal model delta sigma weight residual 1.524 1.539 -0.016 1.29e-02 6.01e+03 1.50e+00 ... (remaining 12199 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.05: 308 107.05 - 113.79: 14717 113.79 - 120.52: 4072 120.52 - 127.26: 2985 127.26 - 133.99: 78 Bond angle restraints: 22160 Sorted by residual: angle pdb=" C09 E7O B 701 " pdb=" C10 E7O B 701 " pdb=" N11 E7O B 701 " ideal model delta sigma weight residual 81.04 121.63 -40.59 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C09 E7O A 701 " pdb=" C10 E7O A 701 " pdb=" N11 E7O A 701 " ideal model delta sigma weight residual 81.04 121.58 -40.54 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C04 E7O B 701 " pdb=" C10 E7O B 701 " pdb=" N11 E7O B 701 " ideal model delta sigma weight residual 155.44 119.21 36.23 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C04 E7O A 701 " pdb=" C10 E7O A 701 " pdb=" N11 E7O A 701 " ideal model delta sigma weight residual 155.44 119.28 36.16 3.00e+00 1.11e-01 1.45e+02 angle pdb=" N ASN B 112 " pdb=" CA ASN B 112 " pdb=" C ASN B 112 " ideal model delta sigma weight residual 108.41 102.31 6.10 1.61e+00 3.86e-01 1.43e+01 ... (remaining 22155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 4432 16.79 - 33.58: 359 33.58 - 50.37: 55 50.37 - 67.15: 14 67.15 - 83.94: 2 Dihedral angle restraints: 4862 sinusoidal: 2218 harmonic: 2644 Sorted by residual: dihedral pdb=" CA PHE A 49 " pdb=" C PHE A 49 " pdb=" N ALA A 50 " pdb=" CA ALA A 50 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PHE B 49 " pdb=" C PHE B 49 " pdb=" N ALA B 50 " pdb=" CA ALA B 50 " ideal model delta harmonic sigma weight residual -180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CG ARG B 29 " pdb=" CD ARG B 29 " pdb=" NE ARG B 29 " pdb=" CZ ARG B 29 " ideal model delta sinusoidal sigma weight residual -180.00 -135.46 -44.54 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 4859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 765 0.038 - 0.076: 165 0.076 - 0.115: 54 0.115 - 0.153: 4 0.153 - 0.191: 2 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA ASN B 112 " pdb=" N ASN B 112 " pdb=" C ASN B 112 " pdb=" CB ASN B 112 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA ASN A 112 " pdb=" N ASN A 112 " pdb=" C ASN A 112 " pdb=" CB ASN A 112 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA PRO A 16 " pdb=" N PRO A 16 " pdb=" C PRO A 16 " pdb=" CB PRO A 16 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 987 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 112 " -0.080 2.00e-02 2.50e+03 7.86e-02 9.27e+01 pdb=" CG ASN B 112 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN B 112 " 0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN B 112 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 112 " 0.110 2.00e-02 2.50e+03 pdb="HD22 ASN B 112 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 112 " -0.077 2.00e-02 2.50e+03 7.53e-02 8.51e+01 pdb=" CG ASN A 112 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 112 " 0.073 2.00e-02 2.50e+03 pdb=" ND2 ASN A 112 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 112 " 0.106 2.00e-02 2.50e+03 pdb="HD22 ASN A 112 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 569 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.66e+00 pdb=" N PRO B 570 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " -0.027 5.00e-02 4.00e+02 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 653 2.21 - 2.80: 24715 2.80 - 3.40: 33142 3.40 - 4.00: 42912 4.00 - 4.60: 67426 Nonbonded interactions: 168848 Sorted by model distance: nonbonded pdb=" O GLU B 178 " pdb="HH12 ARG B 489 " model vdw 1.607 1.850 nonbonded pdb=" HH TYR A 18 " pdb=" O MET A 624 " model vdw 1.607 1.850 nonbonded pdb=" O GLU A 178 " pdb="HH12 ARG A 489 " model vdw 1.608 1.850 nonbonded pdb=" HH TYR B 18 " pdb=" O MET B 624 " model vdw 1.609 1.850 nonbonded pdb=" O LEU B 23 " pdb=" HG SER B 27 " model vdw 1.615 1.850 ... (remaining 168843 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' } 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: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 3938 2.51 5 N 940 2.21 5 O 998 1.98 5 H 6138 0.53 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: 0.700 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: 0.170 Extract box with map and model: 3.990 Check model and map are aligned: 0.160 Process input model: 40.180 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6066 Z= 0.181 Angle : 0.992 40.589 8266 Z= 0.402 Chirality : 0.038 0.191 990 Planarity : 0.005 0.048 998 Dihedral : 12.847 83.944 2122 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 1.70 (0.31), residues: 746 helix: 1.70 (0.22), residues: 560 sheet: -0.12 (0.79), residues: 42 loop : -0.65 (0.55), residues: 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 1.9595 time to fit residues: 266.5822 Evaluate side-chains 84 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN B 514 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 6066 Z= 0.373 Angle : 0.871 13.953 8266 Z= 0.415 Chirality : 0.046 0.198 990 Planarity : 0.007 0.073 998 Dihedral : 5.353 41.382 804 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.30), residues: 746 helix: 1.01 (0.21), residues: 556 sheet: -0.11 (0.74), residues: 42 loop : -0.91 (0.54), residues: 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 115 average time/residue: 1.6847 time to fit residues: 208.0307 Evaluate side-chains 87 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 1.1409 time to fit residues: 7.4609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 6066 Z= 0.234 Angle : 0.660 13.996 8266 Z= 0.314 Chirality : 0.039 0.143 990 Planarity : 0.005 0.049 998 Dihedral : 5.018 32.278 804 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.31), residues: 746 helix: 1.34 (0.22), residues: 558 sheet: 0.01 (0.72), residues: 42 loop : -1.12 (0.56), residues: 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 101 average time/residue: 1.8152 time to fit residues: 195.9857 Evaluate side-chains 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.7296 time to fit residues: 3.8112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 0.0370 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 6066 Z= 0.190 Angle : 0.591 12.888 8266 Z= 0.284 Chirality : 0.038 0.150 990 Planarity : 0.004 0.042 998 Dihedral : 4.794 35.159 804 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.32), residues: 746 helix: 1.64 (0.22), residues: 558 sheet: -0.11 (0.69), residues: 42 loop : -0.77 (0.57), residues: 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 91 average time/residue: 2.0498 time to fit residues: 198.3616 Evaluate side-chains 85 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.6722 time to fit residues: 3.5679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN B 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.7605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 6066 Z= 0.275 Angle : 0.662 15.849 8266 Z= 0.323 Chirality : 0.040 0.145 990 Planarity : 0.005 0.048 998 Dihedral : 5.166 39.133 804 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.31), residues: 746 helix: 1.43 (0.22), residues: 554 sheet: 0.10 (0.69), residues: 42 loop : -1.23 (0.54), residues: 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 99 average time/residue: 2.0572 time to fit residues: 216.1101 Evaluate side-chains 80 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.7206 time to fit residues: 3.6954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7982 moved from start: 0.7967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 6066 Z= 0.211 Angle : 0.608 14.307 8266 Z= 0.295 Chirality : 0.038 0.134 990 Planarity : 0.005 0.048 998 Dihedral : 4.947 35.689 804 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.31), residues: 746 helix: 1.47 (0.22), residues: 554 sheet: 0.08 (0.69), residues: 42 loop : -1.05 (0.56), residues: 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 1.103 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 89 average time/residue: 2.1373 time to fit residues: 201.7664 Evaluate side-chains 84 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.1940 time to fit residues: 2.1135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.7995 moved from start: 0.8339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6066 Z= 0.197 Angle : 0.591 13.431 8266 Z= 0.285 Chirality : 0.037 0.135 990 Planarity : 0.005 0.046 998 Dihedral : 4.755 30.289 804 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.31), residues: 746 helix: 1.57 (0.22), residues: 554 sheet: -0.05 (0.70), residues: 42 loop : -0.92 (0.57), residues: 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.031 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 88 average time/residue: 2.1151 time to fit residues: 197.5002 Evaluate side-chains 87 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1948 time to fit residues: 1.8506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.8608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6066 Z= 0.224 Angle : 0.621 14.293 8266 Z= 0.300 Chirality : 0.038 0.135 990 Planarity : 0.005 0.048 998 Dihedral : 4.894 34.997 804 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.31), residues: 746 helix: 1.52 (0.22), residues: 554 sheet: -0.04 (0.70), residues: 42 loop : -0.96 (0.56), residues: 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.993 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 88 average time/residue: 2.1538 time to fit residues: 201.0257 Evaluate side-chains 85 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.2053 time to fit residues: 2.0124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.2980 chunk 66 optimal weight: 0.1980 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.8636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6066 Z= 0.171 Angle : 0.584 12.819 8266 Z= 0.280 Chirality : 0.036 0.131 990 Planarity : 0.004 0.045 998 Dihedral : 4.663 28.914 804 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.32), residues: 746 helix: 1.66 (0.22), residues: 558 sheet: -0.12 (0.70), residues: 42 loop : -0.64 (0.60), residues: 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.952 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 2.1603 time to fit residues: 196.9739 Evaluate side-chains 88 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1939 time to fit residues: 1.8269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7997 moved from start: 0.8765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6066 Z= 0.169 Angle : 0.571 11.910 8266 Z= 0.275 Chirality : 0.036 0.131 990 Planarity : 0.004 0.045 998 Dihedral : 4.517 25.455 804 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.32), residues: 746 helix: 1.76 (0.22), residues: 558 sheet: -0.22 (0.68), residues: 42 loop : -0.62 (0.60), residues: 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.973 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 88 average time/residue: 2.2241 time to fit residues: 207.3603 Evaluate side-chains 86 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.2001 time to fit residues: 1.4241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.177668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149180 restraints weight = 17496.915| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.15 r_work: 0.3571 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.8790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 6066 Z= 0.148 Angle : 0.555 10.800 8266 Z= 0.267 Chirality : 0.036 0.130 990 Planarity : 0.004 0.044 998 Dihedral : 4.411 21.838 804 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.32), residues: 746 helix: 1.86 (0.22), residues: 558 sheet: -0.30 (0.67), residues: 42 loop : -0.61 (0.60), residues: 146 =============================================================================== Job complete usr+sys time: 4553.32 seconds wall clock time: 80 minutes 51.98 seconds (4851.98 seconds total)