Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:29:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/11_2022/6r4r_4727.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/11_2022/6r4r_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_4727/11_2022/6r4r_4727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/11_2022/6r4r_4727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/11_2022/6r4r_4727.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/11_2022/6r4r_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 stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 2.77, per 1000 atoms: 0.64 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 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 688.3 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. 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: 1.06 Time building geometry restraints manager: 1.65 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. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 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 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.620 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 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 : 0.008 0.057 4403 Z= 0.504 Angle : 1.430 15.584 5943 Z= 0.726 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, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.719 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1506 time to fit residues: 37.6091 Evaluate side-chains 114 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7199 ------------------------------------------------------------------------------- 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: 20.0000 chunk 37 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 25 HIS E 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 4403 Z= 0.203 Angle : 0.741 10.403 5943 Z= 0.361 Chirality : 0.046 0.184 595 Planarity : 0.005 0.037 791 Dihedral : 5.961 15.813 602 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 2.95 % 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: -4.90 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 0.590 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 137 average time/residue: 0.1263 time to fit residues: 22.5730 Evaluate side-chains 113 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0400 time to fit residues: 1.0234 ------------------------------------------------------------------------------- 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: 20.0000 chunk 37 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 30.0000 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 35 optimal weight: 0.1980 chunk 33 optimal weight: 7.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4403 Z= 0.224 Angle : 0.679 10.567 5943 Z= 0.340 Chirality : 0.045 0.159 595 Planarity : 0.004 0.032 791 Dihedral : 5.425 15.238 602 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 3.85 % 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: -4.76 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.426 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 128 average time/residue: 0.1514 time to fit residues: 24.2791 Evaluate side-chains 110 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0403 time to fit residues: 1.2534 ------------------------------------------------------------------------------- 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: 20.0000 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 47 optimal weight: 8.9990 chunk 42 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 4.6188 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4403 Z= 0.215 Angle : 0.630 8.039 5943 Z= 0.319 Chirality : 0.044 0.142 595 Planarity : 0.004 0.030 791 Dihedral : 5.110 14.669 602 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 3.40 % 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: -4.61 (0.26), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.20), residues: 525 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.552 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 117 average time/residue: 0.1468 time to fit residues: 21.8420 Evaluate side-chains 104 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0412 time to fit residues: 1.1332 ------------------------------------------------------------------------------- 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: 7.9990 chunk 19 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 42 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 9 optimal weight: 0.0040 chunk 27 optimal weight: 5.9990 overall best weight: 5.6000 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 4403 Z= 0.240 Angle : 0.646 6.853 5943 Z= 0.329 Chirality : 0.045 0.141 595 Planarity : 0.004 0.029 791 Dihedral : 5.180 14.662 602 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 4.76 % 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 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.497 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 112 average time/residue: 0.1453 time to fit residues: 20.9128 Evaluate side-chains 106 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0424 time to fit residues: 1.6181 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 5 optimal weight: 0.0050 chunk 27 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 overall best weight: 4.2602 ------------------------------------------------------------------------------- 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** F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4403 Z= 0.202 Angle : 0.614 7.873 5943 Z= 0.308 Chirality : 0.044 0.139 595 Planarity : 0.003 0.027 791 Dihedral : 4.996 16.428 602 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer Outliers : 3.85 % 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: -4.58 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.528 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 114 average time/residue: 0.1514 time to fit residues: 21.7776 Evaluate side-chains 101 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0345 time to fit residues: 0.8340 ------------------------------------------------------------------------------- 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: 8.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 30.0000 chunk 29 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 4403 Z= 0.378 Angle : 0.775 8.385 5943 Z= 0.400 Chirality : 0.049 0.149 595 Planarity : 0.005 0.032 791 Dihedral : 5.710 19.658 602 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer Outliers : 5.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.552 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 113 average time/residue: 0.1611 time to fit residues: 22.7612 Evaluate side-chains 109 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0791 time to fit residues: 3.0877 ------------------------------------------------------------------------------- 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: 0.0570 chunk 4 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 44 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 40.0000 overall best weight: 3.0302 ------------------------------------------------------------------------------- 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** D 25 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.6887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4403 Z= 0.188 Angle : 0.626 8.934 5943 Z= 0.310 Chirality : 0.044 0.136 595 Planarity : 0.004 0.039 791 Dihedral : 5.087 19.352 602 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 1.36 % 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: -4.67 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.524 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 107 average time/residue: 0.1695 time to fit residues: 22.6681 Evaluate side-chains 96 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0413 time to fit residues: 0.8355 ------------------------------------------------------------------------------- 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: 5.9990 chunk 41 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 44 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 4403 Z= 0.315 Angle : 0.729 8.223 5943 Z= 0.367 Chirality : 0.047 0.141 595 Planarity : 0.005 0.046 791 Dihedral : 5.385 18.996 602 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % 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: -4.71 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.19), residues: 525 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.522 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 0.1601 time to fit residues: 20.3711 Evaluate side-chains 100 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0414 time to fit residues: 1.0107 ------------------------------------------------------------------------------- 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: 9.9990 chunk 23 optimal weight: 9.9990 chunk 41 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.7301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 4403 Z= 0.247 Angle : 0.686 8.363 5943 Z= 0.341 Chirality : 0.045 0.131 595 Planarity : 0.004 0.039 791 Dihedral : 5.192 18.049 602 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 1.13 % 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 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.499 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 100 average time/residue: 0.1643 time to fit residues: 20.6261 Evaluate side-chains 98 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0477 time to fit residues: 1.0293 ------------------------------------------------------------------------------- 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: 20.0000 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 46 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.179917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.171624 restraints weight = 8461.274| |-----------------------------------------------------------------------------| r_work (start): 0.4811 rms_B_bonded: 2.91 r_work: 0.4805 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4799 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work: 0.4793 rms_B_bonded: 2.70 restraints_weight: 0.1250 r_work: 0.4787 rms_B_bonded: 2.76 restraints_weight: 0.0625 r_work: 0.4780 rms_B_bonded: 2.85 restraints_weight: 0.0312 r_work: 0.4774 rms_B_bonded: 2.97 restraints_weight: 0.0156 r_work: 0.4767 rms_B_bonded: 3.10 restraints_weight: 0.0078 r_work: 0.4759 rms_B_bonded: 3.26 restraints_weight: 0.0039 r_work: 0.4751 rms_B_bonded: 3.43 restraints_weight: 0.0020 r_work: 0.4744 rms_B_bonded: 3.62 restraints_weight: 0.0010 r_work: 0.4735 rms_B_bonded: 3.84 restraints_weight: 0.0005 r_work: 0.4727 rms_B_bonded: 4.07 restraints_weight: 0.0002 r_work: 0.4717 rms_B_bonded: 4.33 restraints_weight: 0.0001 r_work: 0.4708 rms_B_bonded: 4.62 restraints_weight: 0.0001 r_work: 0.4697 rms_B_bonded: 4.93 restraints_weight: 0.0000 r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.7394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 4403 Z= 0.296 Angle : 0.729 8.635 5943 Z= 0.364 Chirality : 0.046 0.142 595 Planarity : 0.005 0.055 791 Dihedral : 5.415 20.338 602 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % 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: -4.78 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.18), residues: 525 =============================================================================== Job complete usr+sys time: 1136.90 seconds wall clock time: 21 minutes 57.95 seconds (1317.95 seconds total)