Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 10:46:10 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/01_2021/6r4r_4727.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/01_2021/6r4r_4727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/01_2021/6r4r_4727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/01_2021/6r4r_4727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/01_2021/6r4r_4727.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/01_2021/6r4r_4727.pdb" } resolution = 3.4 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= 0.011 sd= 0.467 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 "A TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 4312 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "C" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "E" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "G" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Time building chain proxies: 2.61, per 1000 atoms: 0.61 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Number of scatterers: 4312 At special positions: 0 Unit cell: (90.695, 115.005, 44.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 896 8.00 N 686 7.00 C 2723 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 Amimo 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: 1.69 Conformation dependent library (CDL) restraints added in 805.7 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.618A pdb=" N LYS A 16 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLU C 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG A 18 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS C 16 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG C 18 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS E 16 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG E 18 " --> pdb=" O GLU G 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25 removed outlier: 6.538A pdb=" N ASP A 23 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 23 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP E 23 " --> pdb=" O LEU G 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 56 removed outlier: 6.149A pdb=" N GLU A 51 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLY C 54 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 53 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU C 56 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP A 55 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU C 51 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY E 54 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 53 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU E 56 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N TRP C 55 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU E 51 " --> pdb=" O GLU G 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY G 54 " --> pdb=" O GLU E 51 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE E 53 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU G 56 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP E 55 " --> pdb=" O LEU G 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 61 through 68 Processing sheet with id=AA8, first strand: chain 'A' and resid 71 through 76 Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.617A pdb=" N LYS B 16 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU D 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 18 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS D 16 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG D 18 " --> pdb=" O GLU F 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 23 through 25 removed outlier: 6.538A pdb=" N ASP B 23 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP D 23 " --> pdb=" O LEU F 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 29 through 34 Processing sheet with id=AB4, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.151A pdb=" N GLU B 51 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY D 54 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 53 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU D 56 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N TRP B 55 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU D 51 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY F 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 53 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU F 56 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP D 55 " --> pdb=" O LEU F 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 61 through 68 Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 76 110 hydrogen bonds defined for protein. 330 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: 1.20 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1415 1.34 - 1.45: 707 1.45 - 1.57: 2267 1.57 - 1.69: 0 1.69 - 1.80: 14 Bond restraints: 4403 Sorted by residual: bond pdb=" CG LEU C 30 " pdb=" CD1 LEU C 30 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.98e+00 bond pdb=" CG LEU G 30 " pdb=" CD1 LEU G 30 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.94e+00 bond pdb=" CG LEU E 30 " pdb=" CD1 LEU E 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CG LEU A 30 " pdb=" CD1 LEU A 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CG LEU D 30 " pdb=" CD1 LEU D 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.89e+00 ... (remaining 4398 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.91: 99 106.91 - 113.64: 2147 113.64 - 120.36: 1875 120.36 - 127.09: 1766 127.09 - 133.82: 56 Bond angle restraints: 5943 Sorted by residual: angle pdb=" C GLU C 20 " pdb=" N ASP C 21 " pdb=" CA ASP C 21 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C GLU F 20 " pdb=" N ASP F 21 " pdb=" CA ASP F 21 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C GLU E 20 " pdb=" N ASP E 21 " pdb=" CA ASP E 21 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLU G 20 " pdb=" N ASP G 21 " pdb=" CA ASP G 21 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLU D 20 " pdb=" N ASP D 21 " pdb=" CA ASP D 21 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 ... (remaining 5938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.72: 1867 7.72 - 15.43: 499 15.43 - 23.15: 119 23.15 - 30.87: 35 30.87 - 38.59: 35 Dihedral angle restraints: 2555 sinusoidal: 1036 harmonic: 1519 Sorted by residual: dihedral pdb=" CA GLY E 5 " pdb=" C GLY E 5 " pdb=" N TYR E 6 " pdb=" CA TYR E 6 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLY G 5 " pdb=" C GLY G 5 " pdb=" N TYR G 6 " pdb=" CA TYR G 6 " ideal model delta harmonic sigma weight residual -180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLY C 5 " pdb=" C GLY C 5 " pdb=" N TYR C 6 " pdb=" CA TYR C 6 " ideal model delta harmonic sigma weight residual 180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 2552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 405 0.069 - 0.137: 162 0.137 - 0.206: 21 0.206 - 0.275: 0 0.275 - 0.344: 7 Chirality restraints: 595 Sorted by residual: chirality pdb=" CA ASP F 21 " pdb=" N ASP F 21 " pdb=" C ASP F 21 " pdb=" CB ASP F 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ASP D 21 " pdb=" N ASP D 21 " pdb=" C ASP D 21 " pdb=" CB ASP D 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASP A 21 " pdb=" N ASP A 21 " pdb=" C ASP A 21 " pdb=" CB ASP A 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 592 not shown) Planarity restraints: 791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 48 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C ALA C 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA C 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS C 49 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 48 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C ALA E 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA E 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS E 49 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 48 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C ALA G 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA G 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS G 49 " -0.018 2.00e-02 2.50e+03 ... (remaining 788 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1211 2.83 - 3.34: 3397 3.34 - 3.86: 7837 3.86 - 4.38: 8251 4.38 - 4.90: 15637 Nonbonded interactions: 36333 Sorted by model distance: nonbonded pdb=" OE2 GLU A 47 " pdb=" NZ LYS A 49 " model vdw 2.308 2.520 nonbonded pdb=" OE2 GLU B 47 " pdb=" NZ LYS B 49 " model vdw 2.309 2.520 nonbonded pdb=" OE2 GLU F 47 " pdb=" NZ LYS F 49 " model vdw 2.310 2.520 nonbonded pdb=" OE2 GLU E 47 " pdb=" NZ LYS E 49 " model vdw 2.310 2.520 nonbonded pdb=" OE2 GLU C 47 " pdb=" NZ LYS C 49 " model vdw 2.310 2.520 ... (remaining 36328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 4312 4312 False True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 2723 2.51 5 N 686 2.21 5 O 896 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 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: 0.890 Set model interpretation parameters: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.810 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.020 Process input model: 16.660 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.220 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.008 0.057 4403 Angle : 1.430 15.584 5943 Chirality : 0.075 0.344 595 Planarity : 0.008 0.054 791 Dihedral : 10.872 38.585 1617 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % 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: -5.16 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.535 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1607 time to fit residues: 32.7868 Evaluate side-chains 111 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 9.9990 chunk 37 optimal weight: 40.0000 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.038 4403 Angle : 0.712 7.434 5943 Chirality : 0.046 0.142 595 Planarity : 0.005 0.042 791 Dihedral : 5.781 16.524 602 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % 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: -4.91 (0.23), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.18), residues: 525 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.551 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1696 time to fit residues: 24.7333 Evaluate side-chains 107 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 40.0000 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN G 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.032 4403 Angle : 0.757 7.906 5943 Chirality : 0.048 0.156 595 Planarity : 0.005 0.047 791 Dihedral : 5.719 17.846 602 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.18), residues: 525 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.559 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1814 time to fit residues: 23.2362 Evaluate side-chains 97 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 40.0000 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 12 optimal weight: 0.0270 chunk 39 optimal weight: 0.0030 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 overall best weight: 2.9852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.037 4403 Angle : 0.609 6.844 5943 Chirality : 0.043 0.136 595 Planarity : 0.004 0.040 791 Dihedral : 4.821 16.666 602 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % 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: -4.69 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.553 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1478 time to fit residues: 19.5779 Evaluate side-chains 105 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.4980 chunk 19 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 20.0000 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.025 4403 Angle : 0.647 7.344 5943 Chirality : 0.045 0.145 595 Planarity : 0.004 0.037 791 Dihedral : 4.928 17.278 602 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % 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: -4.73 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.591 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1730 time to fit residues: 22.7641 Evaluate side-chains 104 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.0170 chunk 21 optimal weight: 20.0000 chunk 3 optimal weight: 0.0070 chunk 15 optimal weight: 30.0000 chunk 24 optimal weight: 40.0000 chunk 45 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 30.0000 chunk 34 optimal weight: 50.0000 overall best weight: 3.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.025 4403 Angle : 0.639 7.310 5943 Chirality : 0.044 0.133 595 Planarity : 0.004 0.037 791 Dihedral : 4.722 18.069 602 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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: -4.75 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.18), residues: 525 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.542 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1558 time to fit residues: 20.5195 Evaluate side-chains 105 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.0980 chunk 39 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.7155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.025 4403 Angle : 0.677 7.841 5943 Chirality : 0.046 0.187 595 Planarity : 0.004 0.038 791 Dihedral : 4.931 18.008 602 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % 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: -4.71 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.537 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1465 time to fit residues: 18.0288 Evaluate side-chains 96 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 50.0000 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 41 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.7303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.033 4403 Angle : 0.763 8.557 5943 Chirality : 0.050 0.246 595 Planarity : 0.005 0.042 791 Dihedral : 5.464 19.837 602 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % 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: -4.78 (0.23), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.18), residues: 525 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.564 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1297 time to fit residues: 15.0601 Evaluate side-chains 88 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 44 optimal weight: 40.0000 chunk 38 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 GLN F 46 GLN F 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.7510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.025 4403 Angle : 0.677 8.476 5943 Chirality : 0.046 0.174 595 Planarity : 0.004 0.037 791 Dihedral : 4.949 17.857 602 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.534 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1420 time to fit residues: 17.2049 Evaluate side-chains 95 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 50.0000 chunk 23 optimal weight: 50.0000 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 0.0030 chunk 4 optimal weight: 8.9990 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 GLN F 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.7607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.022 4403 Angle : 0.683 8.412 5943 Chirality : 0.047 0.173 595 Planarity : 0.004 0.057 791 Dihedral : 5.032 23.601 602 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.19), residues: 525 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield and 0 Emsley and 525 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.565 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1463 time to fit residues: 16.8616 Evaluate side-chains 91 residues out of total 441 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7206 r_free = 0.7206 target = 0.467192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.7656 r_free = 0.7656 target = 0.403790 restraints weight = 9403.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.7689 r_free = 0.7689 target = 0.405516 restraints weight = 5237.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.7725 r_free = 0.7725 target = 0.406631 restraints weight = 3271.364| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.027 4403 ANGLE : 0.750 9.022 5943 CHIRALITY : 0.050 0.218 595 PLANARITY : 0.004 0.040 791 DIHEDRAL : 5.441 24.956 602 MIN NONBONDED DISTANCE : 2.128 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 13.94 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 8.57 % FAVORED : 91.43 % ROTAMER OUTLIERS : 0.23 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -4.63 (0.24), RESIDUES: 525 HELIX: NONE (NONE), RESIDUES: 0 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -3.53 (0.18), RESIDUES: 525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.7622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.027 4403 Angle : 0.750 9.022 5943 Chirality : 0.050 0.218 595 Planarity : 0.004 0.040 791 Dihedral : 5.441 24.956 602 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.18), residues: 525 =============================================================================== Job complete usr+sys time: 1283.37 seconds wall clock time: 24 minutes 8.52 seconds (1448.52 seconds total)