Starting phenix.real_space_refine (version: dev) on Tue Feb 21 18:20:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/02_2023/7pew_13359.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/02_2023/7pew_13359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/02_2023/7pew_13359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/02_2023/7pew_13359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/02_2023/7pew_13359.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/02_2023/7pew_13359.pdb" } resolution = 4.6 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13304 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3636 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Chain: "I" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3580 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Time building chain proxies: 7.39, per 1000 atoms: 0.56 Number of scatterers: 13304 At special positions: 0 Unit cell: (131.25, 163.8, 117.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 352 15.00 O 3184 8.00 N 2504 7.00 C 7254 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: 7.54 Conformation dependent library (CDL) restraints added in 891.3 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 71.9% alpha, 2.6% beta 173 base pairs and 310 stacking pairs defined. Time for finding SS restraints: 6.39 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.690A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.623A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.583A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.119A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.291A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.500A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.664A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.254A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.216A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.641A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.733A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.602A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.917A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.228A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.026A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 407 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 448 hydrogen bonds 896 hydrogen bond angles 0 basepair planarities 173 basepair parallelities 310 stacking parallelities Total time for adding SS restraints: 6.82 Time building geometry restraints manager: 7.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2350 1.33 - 1.46: 5344 1.46 - 1.58: 5846 1.58 - 1.70: 702 1.70 - 1.83: 20 Bond restraints: 14262 Sorted by residual: bond pdb=" CG GLU D 113 " pdb=" CD GLU D 113 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.29e+00 bond pdb=" C3' DC I 12 " pdb=" O3' DC I 12 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.60e+00 bond pdb=" C3' DG I 140 " pdb=" O3' DG I 140 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 4.00e+00 bond pdb=" C3' DG I 28 " pdb=" O3' DG I 28 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.40e+00 bond pdb=" CD GLU D 113 " pdb=" OE1 GLU D 113 " ideal model delta sigma weight residual 1.249 1.215 0.034 1.90e-02 2.77e+03 3.25e+00 ... (remaining 14257 not shown) Histogram of bond angle deviations from ideal: 97.70 - 104.69: 1425 104.69 - 111.69: 7393 111.69 - 118.68: 3992 118.68 - 125.68: 6814 125.68 - 132.67: 1150 Bond angle restraints: 20774 Sorted by residual: angle pdb=" N GLU D 113 " pdb=" CA GLU D 113 " pdb=" CB GLU D 113 " ideal model delta sigma weight residual 110.28 118.47 -8.19 1.55e+00 4.16e-01 2.79e+01 angle pdb=" N GLU A 105 " pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " ideal model delta sigma weight residual 110.28 118.46 -8.18 1.55e+00 4.16e-01 2.79e+01 angle pdb=" N GLU G 64 " pdb=" CA GLU G 64 " pdb=" CB GLU G 64 " ideal model delta sigma weight residual 110.16 117.31 -7.15 1.48e+00 4.57e-01 2.33e+01 angle pdb=" N GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta sigma weight residual 110.28 117.42 -7.14 1.55e+00 4.16e-01 2.12e+01 angle pdb=" N GLN D 95 " pdb=" CA GLN D 95 " pdb=" CB GLN D 95 " ideal model delta sigma weight residual 110.12 116.69 -6.57 1.47e+00 4.63e-01 2.00e+01 ... (remaining 20769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 5579 35.97 - 71.94: 1738 71.94 - 107.90: 26 107.90 - 143.87: 2 143.87 - 179.84: 3 Dihedral angle restraints: 7348 sinusoidal: 5126 harmonic: 2222 Sorted by residual: dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ARG H 33 " pdb=" C ARG H 33 " pdb=" N LYS H 34 " pdb=" CA LYS H 34 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLU E 59 " pdb=" C GLU E 59 " pdb=" N LEU E 60 " pdb=" CA LEU E 60 " ideal model delta harmonic sigma weight residual 180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 7345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1790 0.050 - 0.100: 451 0.100 - 0.150: 96 0.150 - 0.200: 19 0.200 - 0.251: 4 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CB THR B 54 " pdb=" CA THR B 54 " pdb=" OG1 THR B 54 " pdb=" CG2 THR B 54 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA GLU A 94 " pdb=" N GLU A 94 " pdb=" C GLU A 94 " pdb=" CB GLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PHE A 104 " pdb=" N PHE A 104 " pdb=" C PHE A 104 " pdb=" CB PHE A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2357 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 60 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C ALA G 60 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA G 60 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU G 61 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 113 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" CD GLU D 113 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU D 113 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU D 113 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 106 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" CG ASP E 106 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP E 106 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP E 106 " -0.013 2.00e-02 2.50e+03 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2643 2.78 - 3.31: 12088 3.31 - 3.84: 29169 3.84 - 4.37: 32242 4.37 - 4.90: 44010 Nonbonded interactions: 120152 Sorted by model distance: nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.249 2.520 nonbonded pdb=" O LYS H 116 " pdb=" OG1 THR H 119 " model vdw 2.274 2.440 nonbonded pdb=" O GLN A 93 " pdb=" OG SER A 96 " model vdw 2.279 2.440 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.282 2.520 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.291 2.440 ... (remaining 120147 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 352 5.49 5 S 10 5.16 5 C 7254 2.51 5 N 2504 2.21 5 O 3184 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 6.950 Check model and map are aligned: 0.190 Process input model: 44.470 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 : 0.006 0.064 14262 Z= 0.335 Angle : 0.912 11.014 20774 Z= 0.518 Chirality : 0.048 0.251 2360 Planarity : 0.007 0.075 1408 Dihedral : 30.235 179.839 5916 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -0.20 (0.27), residues: 752 helix: 0.18 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -0.58 (0.35), residues: 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2647 time to fit residues: 63.6866 Evaluate side-chains 107 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 109 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 14262 Z= 0.340 Angle : 0.678 10.484 20774 Z= 0.401 Chirality : 0.037 0.134 2360 Planarity : 0.005 0.053 1408 Dihedral : 33.548 178.881 4392 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 752 helix: 1.14 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.2783 time to fit residues: 54.8697 Evaluate side-chains 94 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1457 time to fit residues: 1.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN C 112 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.055 14262 Z= 0.470 Angle : 0.782 12.412 20774 Z= 0.455 Chirality : 0.041 0.184 2360 Planarity : 0.006 0.049 1408 Dihedral : 34.032 178.154 4392 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 29.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.29), residues: 752 helix: 0.84 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -0.44 (0.38), residues: 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.2704 time to fit residues: 47.2859 Evaluate side-chains 85 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 14262 Z= 0.282 Angle : 0.655 9.415 20774 Z= 0.389 Chirality : 0.036 0.158 2360 Planarity : 0.004 0.040 1408 Dihedral : 33.726 179.688 4392 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.29), residues: 752 helix: 1.34 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -0.33 (0.38), residues: 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.2682 time to fit residues: 49.4780 Evaluate side-chains 93 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 14262 Z= 0.240 Angle : 0.635 8.162 20774 Z= 0.376 Chirality : 0.035 0.144 2360 Planarity : 0.004 0.045 1408 Dihedral : 33.431 179.715 4392 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.30), residues: 752 helix: 1.45 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.20 (0.39), residues: 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2636 time to fit residues: 48.7572 Evaluate side-chains 92 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 14262 Z= 0.329 Angle : 0.682 9.955 20774 Z= 0.400 Chirality : 0.036 0.167 2360 Planarity : 0.005 0.056 1408 Dihedral : 33.505 178.633 4392 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.30), residues: 752 helix: 1.33 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.20 (0.39), residues: 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 126 average time/residue: 0.2719 time to fit residues: 49.4975 Evaluate side-chains 96 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1474 time to fit residues: 1.3794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 61 optimal weight: 8.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 14262 Z= 0.266 Angle : 0.662 8.701 20774 Z= 0.391 Chirality : 0.036 0.172 2360 Planarity : 0.004 0.056 1408 Dihedral : 33.426 179.626 4392 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.30), residues: 752 helix: 1.24 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.18 (0.40), residues: 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2521 time to fit residues: 45.9455 Evaluate side-chains 96 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 63 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14262 Z= 0.186 Angle : 0.639 9.151 20774 Z= 0.378 Chirality : 0.035 0.148 2360 Planarity : 0.004 0.057 1408 Dihedral : 32.997 179.176 4392 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.30), residues: 752 helix: 1.40 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.25 (0.39), residues: 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.2434 time to fit residues: 50.5150 Evaluate side-chains 103 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 29 optimal weight: 0.1980 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 14262 Z= 0.301 Angle : 0.673 8.935 20774 Z= 0.396 Chirality : 0.036 0.158 2360 Planarity : 0.005 0.056 1408 Dihedral : 33.191 178.249 4392 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.30), residues: 752 helix: 1.36 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2498 time to fit residues: 45.1518 Evaluate side-chains 97 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 14262 Z= 0.247 Angle : 0.660 8.423 20774 Z= 0.388 Chirality : 0.035 0.207 2360 Planarity : 0.004 0.057 1408 Dihedral : 33.168 178.898 4392 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.30), residues: 752 helix: 1.15 (0.23), residues: 536 sheet: None (None), residues: 0 loop : -0.19 (0.40), residues: 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2530 time to fit residues: 44.3212 Evaluate side-chains 100 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.028318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.021277 restraints weight = 182820.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.022032 restraints weight = 88641.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.022581 restraints weight = 54255.619| |-----------------------------------------------------------------------------| r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 14262 Z= 0.201 Angle : 0.640 8.218 20774 Z= 0.376 Chirality : 0.035 0.212 2360 Planarity : 0.004 0.059 1408 Dihedral : 32.999 178.980 4392 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 1.13 (0.30), residues: 752 helix: 1.23 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -0.29 (0.39), residues: 218 =============================================================================== Job complete usr+sys time: 1804.11 seconds wall clock time: 34 minutes 11.96 seconds (2051.96 seconds total)