Starting phenix.real_space_refine on Sun Dec 10 00:16:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/12_2023/7xzy_33534.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/12_2023/7xzy_33534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/12_2023/7xzy_33534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/12_2023/7xzy_33534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/12_2023/7xzy_33534.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/12_2023/7xzy_33534.pdb" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 330 5.49 5 S 14 5.16 5 C 7015 2.51 5 N 2417 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12821 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3372 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "J" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3393 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Time building chain proxies: 7.26, per 1000 atoms: 0.57 Number of scatterers: 12821 At special positions: 0 Unit cell: (127.6, 151.8, 105.6, 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 14 16.00 P 330 15.00 O 3045 8.00 N 2417 7.00 C 7015 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: 7.65 Conformation dependent library (CDL) restraints added in 1.3 seconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 73.5% alpha, 2.4% beta 163 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 6.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.654A 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 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.345A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (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 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.175A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 4.127A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.536A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.519A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.152A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.723A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (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 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.306A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.699A 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 removed outlier: 3.602A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 removed outlier: 4.222A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 removed outlier: 3.639A pdb=" N THR C 101 " --> pdb=" O THR F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.771A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (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: 7.555A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 removed outlier: 3.735A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 410 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 842 hydrogen bond angles 0 basepair planarities 163 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 4.71 Time building geometry restraints manager: 7.98 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: 2094 1.33 - 1.45: 4796 1.45 - 1.57: 6152 1.57 - 1.69: 658 1.69 - 1.81: 24 Bond restraints: 13724 Sorted by residual: bond pdb=" N ILE H 66 " pdb=" CA ILE H 66 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ASN H 81 " pdb=" CA ASN H 81 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.26e-02 6.30e+03 8.21e+00 bond pdb=" N ILE G 87 " pdb=" CA ILE G 87 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.21e-02 6.83e+03 6.56e+00 bond pdb=" N ILE D 66 " pdb=" CA ILE D 66 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.17e-02 7.31e+03 6.21e+00 bond pdb=" N LYS C 118 " pdb=" CA LYS C 118 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.23e-02 6.61e+03 4.51e+00 ... (remaining 13719 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.32: 1425 105.32 - 112.18: 7550 112.18 - 119.04: 3616 119.04 - 125.90: 6289 125.90 - 132.76: 1068 Bond angle restraints: 19948 Sorted by residual: angle pdb=" CA ILE D 66 " pdb=" C ILE D 66 " pdb=" O ILE D 66 " ideal model delta sigma weight residual 121.17 117.11 4.06 1.06e+00 8.90e-01 1.47e+01 angle pdb=" N ILE D 66 " pdb=" CA ILE D 66 " pdb=" C ILE D 66 " ideal model delta sigma weight residual 110.42 107.00 3.42 9.60e-01 1.09e+00 1.27e+01 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" CA GLU A 73 " pdb=" CB GLU A 73 " pdb=" CG GLU A 73 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" C ALA C 86 " pdb=" N ILE C 87 " pdb=" CA ILE C 87 " ideal model delta sigma weight residual 120.56 116.25 4.31 1.28e+00 6.10e-01 1.14e+01 ... (remaining 19943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4731 17.96 - 35.91: 1186 35.91 - 53.87: 1116 53.87 - 71.82: 317 71.82 - 89.78: 23 Dihedral angle restraints: 7373 sinusoidal: 5169 harmonic: 2204 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -163.93 -16.07 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA ILE G 87 " pdb=" CB ILE G 87 " pdb=" CG1 ILE G 87 " pdb=" CD1 ILE G 87 " ideal model delta sinusoidal sigma weight residual 180.00 124.96 55.04 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -138.82 -41.18 2 1.50e+01 4.44e-03 9.25e+00 ... (remaining 7370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2042 0.061 - 0.123: 209 0.123 - 0.184: 10 0.184 - 0.245: 1 0.245 - 0.306: 2 Chirality restraints: 2264 Sorted by residual: chirality pdb=" CB ILE B 29 " pdb=" CA ILE B 29 " pdb=" CG1 ILE B 29 " pdb=" CG2 ILE B 29 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ILE C 87 " pdb=" N ILE C 87 " pdb=" C ILE C 87 " pdb=" CB ILE C 87 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2261 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 64 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" C ASN B 64 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN B 64 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL B 65 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 62 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C LEU B 62 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU B 62 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU B 63 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 69 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C ALA B 69 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA B 69 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 70 " -0.014 2.00e-02 2.50e+03 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 199 2.63 - 3.20: 10916 3.20 - 3.76: 24685 3.76 - 4.33: 30688 4.33 - 4.90: 43141 Nonbonded interactions: 109629 Sorted by model distance: nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 68 " model vdw 2.062 2.440 nonbonded pdb=" O ARG C 20 " pdb=" NZ LYS D 117 " model vdw 2.080 2.520 nonbonded pdb=" OG SER B 47 " pdb=" OP1 DC J 105 " model vdw 2.136 2.440 nonbonded pdb=" O2 DC I 73 " pdb=" N2 DG J 121 " model vdw 2.162 2.496 nonbonded pdb=" NH2 ARG H 30 " pdb=" OP2 DA I 146 " model vdw 2.222 2.520 ... (remaining 109624 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' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.860 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 43.170 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 : 0.004 0.041 13724 Z= 0.227 Angle : 0.688 8.112 19948 Z= 0.424 Chirality : 0.039 0.306 2264 Planarity : 0.005 0.039 1381 Dihedral : 27.844 89.778 5953 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.16 % Allowed : 0.79 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.28), residues: 746 helix: 1.20 (0.20), residues: 542 sheet: None (None), residues: 0 loop : -0.54 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.018 0.002 PHE G 25 TYR 0.023 0.002 TYR C 50 ARG 0.005 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 0.837 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.2399 time to fit residues: 62.7778 Evaluate side-chains 142 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN E 93 GLN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13724 Z= 0.225 Angle : 0.630 10.009 19948 Z= 0.369 Chirality : 0.036 0.188 2264 Planarity : 0.005 0.047 1381 Dihedral : 31.523 89.566 4432 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.41 % Allowed : 9.92 % Favored : 85.67 % 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: 2.12 (0.29), residues: 746 helix: 2.10 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.54 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 31 PHE 0.021 0.002 PHE E 67 TYR 0.026 0.003 TYR F 88 ARG 0.011 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 0.979 Fit side-chains outliers start: 28 outliers final: 10 residues processed: 174 average time/residue: 0.2276 time to fit residues: 58.3373 Evaluate side-chains 131 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1380 time to fit residues: 3.3886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 93 GLN E 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.9272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 13724 Z= 0.352 Angle : 0.788 12.597 19948 Z= 0.455 Chirality : 0.042 0.307 2264 Planarity : 0.007 0.048 1381 Dihedral : 31.972 99.865 4432 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.25 % Allowed : 15.12 % Favored : 80.63 % 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: 1.32 (0.29), residues: 746 helix: 1.67 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -1.32 (0.38), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS B 75 PHE 0.015 0.002 PHE A 78 TYR 0.025 0.003 TYR B 88 ARG 0.010 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 0.941 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 159 average time/residue: 0.2818 time to fit residues: 61.9188 Evaluate side-chains 117 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1541 time to fit residues: 3.9039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 27 optimal weight: 0.0270 chunk 83 optimal weight: 8.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.9787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13724 Z= 0.233 Angle : 0.627 11.934 19948 Z= 0.366 Chirality : 0.035 0.132 2264 Planarity : 0.005 0.055 1381 Dihedral : 31.414 90.014 4432 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.94 % Allowed : 17.64 % Favored : 81.42 % 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: 2.19 (0.30), residues: 746 helix: 2.41 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.39 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR F 88 ARG 0.019 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 0.869 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 129 average time/residue: 0.2863 time to fit residues: 51.4526 Evaluate side-chains 105 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1089 time to fit residues: 1.9292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 1.0191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13724 Z= 0.191 Angle : 0.593 13.232 19948 Z= 0.345 Chirality : 0.033 0.155 2264 Planarity : 0.004 0.055 1381 Dihedral : 31.116 89.596 4432 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.42 % Allowed : 18.74 % Favored : 79.84 % 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: 2.51 (0.31), residues: 746 helix: 2.65 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.26 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.025 0.002 TYR B 88 ARG 0.011 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 128 average time/residue: 0.2509 time to fit residues: 46.0365 Evaluate side-chains 112 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2350 time to fit residues: 2.7426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 1.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13724 Z= 0.229 Angle : 0.623 14.400 19948 Z= 0.361 Chirality : 0.034 0.176 2264 Planarity : 0.004 0.052 1381 Dihedral : 31.074 89.357 4432 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.26 % Allowed : 21.42 % Favored : 77.32 % 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: 2.37 (0.31), residues: 746 helix: 2.56 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -1.45 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.036 0.002 TYR D 80 ARG 0.006 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.928 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 117 average time/residue: 0.2764 time to fit residues: 45.6314 Evaluate side-chains 108 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1243 time to fit residues: 1.9627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 0.0000 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 1.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13724 Z= 0.228 Angle : 0.613 10.590 19948 Z= 0.357 Chirality : 0.033 0.195 2264 Planarity : 0.004 0.053 1381 Dihedral : 30.970 89.448 4432 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.94 % Allowed : 22.99 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.31), residues: 746 helix: 2.62 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -1.52 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.042 0.001 TYR D 80 ARG 0.005 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.982 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 0.2614 time to fit residues: 41.7293 Evaluate side-chains 103 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1281 time to fit residues: 1.8039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 1.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13724 Z= 0.390 Angle : 0.745 14.365 19948 Z= 0.428 Chirality : 0.039 0.212 2264 Planarity : 0.005 0.049 1381 Dihedral : 31.188 86.633 4432 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.89 % Allowed : 22.52 % Favored : 75.59 % 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: 1.69 (0.31), residues: 746 helix: 2.13 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -1.90 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.052 0.002 TYR D 80 ARG 0.004 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.962 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 0.2654 time to fit residues: 41.8445 Evaluate side-chains 105 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1164 time to fit residues: 2.9737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN G 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 1.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13724 Z= 0.361 Angle : 0.714 16.483 19948 Z= 0.409 Chirality : 0.037 0.205 2264 Planarity : 0.005 0.049 1381 Dihedral : 30.976 89.973 4432 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.79 % Allowed : 23.31 % Favored : 75.91 % 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: 1.79 (0.31), residues: 746 helix: 2.29 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.06 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 75 PHE 0.010 0.001 PHE F 100 TYR 0.045 0.002 TYR F 88 ARG 0.004 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.015 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 100 average time/residue: 0.2632 time to fit residues: 37.7112 Evaluate side-chains 97 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1269 time to fit residues: 1.5359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 1.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13724 Z= 0.220 Angle : 0.648 16.198 19948 Z= 0.372 Chirality : 0.034 0.195 2264 Planarity : 0.004 0.053 1381 Dihedral : 30.806 89.291 4432 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.31 % Allowed : 24.09 % Favored : 75.59 % 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: 2.20 (0.32), residues: 746 helix: 2.58 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.007 0.001 PHE E 67 TYR 0.049 0.002 TYR F 88 ARG 0.004 0.000 ARG E 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 1.003 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 107 average time/residue: 0.2551 time to fit residues: 39.3849 Evaluate side-chains 103 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1301 time to fit residues: 1.5360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 72 optimal weight: 40.0000 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.060609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.038271 restraints weight = 85134.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.039174 restraints weight = 45324.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.039693 restraints weight = 30968.626| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 1.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13724 Z= 0.264 Angle : 0.669 15.914 19948 Z= 0.384 Chirality : 0.034 0.203 2264 Planarity : 0.004 0.051 1381 Dihedral : 30.786 89.168 4432 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.16 % Allowed : 24.72 % Favored : 75.12 % 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: 2.19 (0.32), residues: 746 helix: 2.57 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.93 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 46 PHE 0.008 0.001 PHE E 67 TYR 0.043 0.002 TYR F 88 ARG 0.003 0.000 ARG E 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.33 seconds wall clock time: 35 minutes 46.75 seconds (2146.75 seconds total)