Starting phenix.real_space_refine on Sun Dec 10 21:17:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/12_2023/7pf5_13368.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/12_2023/7pf5_13368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/12_2023/7pf5_13368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/12_2023/7pf5_13368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/12_2023/7pf5_13368.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/12_2023/7pf5_13368.pdb" } resolution = 3.8 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= 0.001 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 334 5.49 5 S 10 5.16 5 C 7420 2.51 5 N 2528 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 105": "OE1" <-> "OE2" Residue "b GLU 53": "OE1" <-> "OE2" Residue "b TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 61": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c GLU 92": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 76": "OE1" <-> "OE2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "e TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 105": "OE1" <-> "OE2" Residue "f ASP 24": "OD1" <-> "OD2" Residue "f GLU 53": "OE1" <-> "OE2" Residue "g GLU 41": "OE1" <-> "OE2" Residue "h TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 76": "OE1" <-> "OE2" Residue "h TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 41": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13470 Number of models: 1 Model: "" Number of chains: 11 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: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3442 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3405 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "u" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 7.48, per 1000 atoms: 0.56 Number of scatterers: 13470 At special positions: 0 Unit cell: (99.75, 133.35, 126, 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 334 15.00 O 3178 8.00 N 2528 7.00 C 7420 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: 7.93 Conformation dependent library (CDL) restraints added in 1.4 seconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 69.6% alpha, 2.6% beta 165 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 7.35 Creating SS restraints... Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.568A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE a 78 " --> pdb=" O ILE a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 removed outlier: 3.549A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 42 Processing helix chain 'b' and resid 49 through 77 removed outlier: 4.024A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.566A pdb=" N GLN b 93 " --> pdb=" O ALA b 89 " (cutoff:3.500A) 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: 4.247A 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 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 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 77 removed outlier: 3.555A 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 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.951A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.572A pdb=" N GLN f 93 " --> pdb=" O ALA f 89 " (cutoff:3.500A) 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: 4.020A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 removed outlier: 3.507A pdb=" N ASN g 89 " --> pdb=" O LEU g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 37 through 49 removed outlier: 3.711A pdb=" N VAL h 41 " --> pdb=" O TYR h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 84 removed outlier: 3.528A 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 removed outlier: 3.677A pdb=" N LYS h 108 " --> pdb=" O GLY h 104 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 51 removed outlier: 3.991A pdb=" N LEU u 42 " --> pdb=" O PRO u 38 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER u 50 " --> pdb=" O ALA u 46 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS u 51 " --> pdb=" O VAL u 47 " (cutoff:3.500A) Processing helix chain 'u' and resid 58 through 69 Processing helix chain 'u' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.871A 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: 3.500A 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 'c' and resid 42 through 43 removed outlier: 7.183A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.925A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.331A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'u' and resid 56 through 57 433 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 846 hydrogen bond angles 0 basepair planarities 165 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 6.88 Time building geometry restraints manager: 8.23 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: 2457 1.33 - 1.45: 4977 1.45 - 1.58: 6266 1.58 - 1.70: 666 1.70 - 1.82: 20 Bond restraints: 14386 Sorted by residual: bond pdb=" C3' DG J 541 " pdb=" O3' DG J 541 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.31e+00 bond pdb=" C3' DG I 335 " pdb=" O3' DG I 335 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.30e+00 bond pdb=" CG GLU b 53 " pdb=" CD GLU b 53 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.10e+00 bond pdb=" CB GLU b 53 " pdb=" CG GLU b 53 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.06e+00 bond pdb=" C3' DG I 223 " pdb=" O3' DG I 223 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.50e+00 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 96.08 - 103.41: 838 103.41 - 110.75: 6226 110.75 - 118.08: 5502 118.08 - 125.42: 7163 125.42 - 132.75: 1124 Bond angle restraints: 20853 Sorted by residual: angle pdb=" CB ARG c 42 " pdb=" CG ARG c 42 " pdb=" CD ARG c 42 " ideal model delta sigma weight residual 111.30 121.64 -10.34 2.30e+00 1.89e-01 2.02e+01 angle pdb=" C TYR e 54 " pdb=" N GLN e 55 " pdb=" CA GLN e 55 " ideal model delta sigma weight residual 120.31 114.28 6.03 1.52e+00 4.33e-01 1.57e+01 angle pdb=" N GLN e 55 " pdb=" CA GLN e 55 " pdb=" CB GLN e 55 " ideal model delta sigma weight residual 110.28 116.01 -5.73 1.55e+00 4.16e-01 1.37e+01 angle pdb=" CB MET b 84 " pdb=" CG MET b 84 " pdb=" SD MET b 84 " ideal model delta sigma weight residual 112.70 123.54 -10.84 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CB MET h 62 " pdb=" CG MET h 62 " pdb=" SD MET h 62 " ideal model delta sigma weight residual 112.70 123.36 -10.66 3.00e+00 1.11e-01 1.26e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 6119 35.82 - 71.64: 1652 71.64 - 107.45: 24 107.45 - 143.27: 1 143.27 - 179.09: 3 Dihedral angle restraints: 7799 sinusoidal: 5368 harmonic: 2431 Sorted by residual: dihedral pdb=" CA TYR e 54 " pdb=" C TYR e 54 " pdb=" N GLN e 55 " pdb=" CA GLN e 55 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR d 88 " pdb=" C THR d 88 " pdb=" N ILE d 89 " pdb=" CA ILE d 89 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DG I 335 " pdb=" C3' DG I 335 " pdb=" O3' DG I 335 " pdb=" P DT I 336 " ideal model delta sinusoidal sigma weight residual -140.00 39.09 -179.09 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1769 0.048 - 0.096: 476 0.096 - 0.144: 103 0.144 - 0.192: 20 0.192 - 0.239: 8 Chirality restraints: 2376 Sorted by residual: chirality pdb=" CA GLN e 55 " pdb=" N GLN e 55 " pdb=" C GLN e 55 " pdb=" CB GLN e 55 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE d 89 " pdb=" CA ILE d 89 " pdb=" CG1 ILE d 89 " pdb=" CG2 ILE d 89 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU a 92 " pdb=" CB LEU a 92 " pdb=" CD1 LEU a 92 " pdb=" CD2 LEU a 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2373 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE e 51 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ILE e 51 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE e 51 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG e 52 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL f 70 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C VAL f 70 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL f 70 " 0.019 2.00e-02 2.50e+03 pdb=" N THR f 71 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 99 " 0.206 9.50e-02 1.11e+02 9.27e-02 6.37e+00 pdb=" NE ARG d 99 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG d 99 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG d 99 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG d 99 " 0.001 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2832 2.79 - 3.32: 12441 3.32 - 3.85: 28918 3.85 - 4.37: 31999 4.37 - 4.90: 44664 Nonbonded interactions: 120854 Sorted by model distance: nonbonded pdb=" O TYR c 39 " pdb=" OG SER d 78 " model vdw 2.264 2.440 nonbonded pdb=" NH2 ARG c 81 " pdb=" O GLN e 55 " model vdw 2.273 2.520 nonbonded pdb=" NH1 ARG g 29 " pdb=" OE2 GLU h 35 " model vdw 2.295 2.520 nonbonded pdb=" ND2 ASN a 108 " pdb=" O GLY b 42 " model vdw 2.296 2.520 nonbonded pdb=" O THR g 16 " pdb=" OG SER g 19 " model vdw 2.296 2.440 ... (remaining 120849 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 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: 3.240 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: 0.000 Extract box with map and model: 3.880 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 47.500 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 0.071 14386 Z= 0.352 Angle : 0.889 10.836 20853 Z= 0.497 Chirality : 0.048 0.239 2376 Planarity : 0.007 0.093 1478 Dihedral : 28.940 179.090 6233 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.59 (0.26), residues: 825 helix: -0.07 (0.19), residues: 573 sheet: -0.81 (1.73), residues: 10 loop : -0.85 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS f 75 PHE 0.043 0.002 PHE e 104 TYR 0.034 0.004 TYR a 54 ARG 0.018 0.001 ARG d 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.086 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2805 time to fit residues: 59.8661 Evaluate side-chains 96 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS ** d 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14386 Z= 0.220 Angle : 0.632 9.600 20853 Z= 0.370 Chirality : 0.035 0.171 2376 Planarity : 0.004 0.055 1478 Dihedral : 31.681 178.571 4581 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.58 % Allowed : 9.67 % Favored : 89.75 % 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: 0.63 (0.27), residues: 825 helix: 0.87 (0.20), residues: 586 sheet: -0.39 (1.86), residues: 10 loop : -0.52 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS h 109 PHE 0.007 0.001 PHE e 104 TYR 0.024 0.002 TYR h 83 ARG 0.005 0.000 ARG c 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.007 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 122 average time/residue: 0.2700 time to fit residues: 47.2834 Evaluate side-chains 99 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1152 time to fit residues: 2.0366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14386 Z= 0.298 Angle : 0.640 10.104 20853 Z= 0.375 Chirality : 0.035 0.157 2376 Planarity : 0.004 0.057 1478 Dihedral : 31.649 175.341 4581 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.44 % Allowed : 11.26 % Favored : 87.30 % 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: 1.06 (0.28), residues: 825 helix: 1.24 (0.21), residues: 586 sheet: -0.67 (1.85), residues: 10 loop : -0.50 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS f 75 PHE 0.010 0.001 PHE g 25 TYR 0.018 0.002 TYR h 83 ARG 0.004 0.001 ARG f 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 110 average time/residue: 0.2816 time to fit residues: 44.3851 Evaluate side-chains 93 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1242 time to fit residues: 2.5602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14386 Z= 0.296 Angle : 0.641 10.639 20853 Z= 0.374 Chirality : 0.035 0.189 2376 Planarity : 0.004 0.058 1478 Dihedral : 31.693 176.148 4581 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.15 % Allowed : 13.71 % Favored : 85.14 % 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: 1.14 (0.28), residues: 825 helix: 1.25 (0.21), residues: 586 sheet: -0.38 (2.02), residues: 10 loop : -0.32 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS f 75 PHE 0.010 0.001 PHE g 25 TYR 0.027 0.002 TYR b 88 ARG 0.005 0.001 ARG a 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 115 average time/residue: 0.2829 time to fit residues: 46.2701 Evaluate side-chains 98 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1325 time to fit residues: 2.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14386 Z= 0.257 Angle : 0.624 11.448 20853 Z= 0.364 Chirality : 0.034 0.176 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.642 176.240 4581 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.01 % Allowed : 15.73 % Favored : 83.26 % 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 (0.28), residues: 825 helix: 1.30 (0.21), residues: 588 sheet: -0.76 (1.88), residues: 10 loop : -0.28 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS f 75 PHE 0.007 0.001 PHE a 104 TYR 0.015 0.002 TYR h 83 ARG 0.004 0.000 ARG c 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 110 average time/residue: 0.2799 time to fit residues: 44.0496 Evaluate side-chains 97 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1465 time to fit residues: 2.0116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 76 GLN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14386 Z= 0.194 Angle : 0.618 11.267 20853 Z= 0.356 Chirality : 0.034 0.198 2376 Planarity : 0.004 0.057 1478 Dihedral : 31.415 176.319 4581 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.72 % Allowed : 18.04 % Favored : 81.24 % 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: 1.36 (0.28), residues: 825 helix: 1.39 (0.21), residues: 586 sheet: -1.00 (1.70), residues: 10 loop : -0.14 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS f 75 PHE 0.016 0.001 PHE d 65 TYR 0.014 0.002 TYR b 88 ARG 0.002 0.000 ARG g 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 127 average time/residue: 0.3045 time to fit residues: 56.2901 Evaluate side-chains 105 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1591 time to fit residues: 1.9998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14386 Z= 0.228 Angle : 0.617 11.293 20853 Z= 0.359 Chirality : 0.034 0.160 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.456 176.487 4581 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.44 % Allowed : 20.06 % Favored : 78.50 % 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: 1.26 (0.28), residues: 825 helix: 1.33 (0.21), residues: 586 sheet: -1.00 (1.65), residues: 10 loop : -0.23 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS f 75 PHE 0.007 0.001 PHE h 65 TYR 0.035 0.002 TYR h 83 ARG 0.003 0.000 ARG c 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 113 average time/residue: 0.2997 time to fit residues: 48.0780 Evaluate side-chains 104 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1344 time to fit residues: 3.0168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN f 93 GLN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 14386 Z= 0.391 Angle : 0.714 11.869 20853 Z= 0.411 Chirality : 0.038 0.198 2376 Planarity : 0.005 0.054 1478 Dihedral : 32.015 176.450 4581 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.01 % Allowed : 20.06 % Favored : 78.93 % 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: 0.67 (0.28), residues: 825 helix: 0.90 (0.21), residues: 584 sheet: -1.26 (1.73), residues: 10 loop : -0.46 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS f 75 PHE 0.010 0.002 PHE a 104 TYR 0.052 0.003 TYR h 83 ARG 0.006 0.001 ARG c 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.074 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 102 average time/residue: 0.2978 time to fit residues: 43.0932 Evaluate side-chains 94 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1219 time to fit residues: 1.6575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 ASN f 93 GLN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14386 Z= 0.265 Angle : 0.671 11.822 20853 Z= 0.385 Chirality : 0.036 0.197 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.812 177.465 4581 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.29 % Allowed : 21.65 % Favored : 78.07 % 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: 0.82 (0.28), residues: 825 helix: 1.02 (0.21), residues: 584 sheet: -1.47 (1.60), residues: 10 loop : -0.41 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS f 75 PHE 0.008 0.001 PHE g 25 TYR 0.044 0.002 TYR h 83 ARG 0.004 0.000 ARG c 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.2743 time to fit residues: 41.5479 Evaluate side-chains 97 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14386 Z= 0.351 Angle : 0.711 11.965 20853 Z= 0.408 Chirality : 0.038 0.198 2376 Planarity : 0.005 0.054 1478 Dihedral : 31.986 177.168 4581 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.58 % Allowed : 20.49 % Favored : 78.93 % 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: 0.56 (0.28), residues: 825 helix: 0.81 (0.21), residues: 586 sheet: -1.67 (1.63), residues: 10 loop : -0.46 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS f 75 PHE 0.008 0.002 PHE g 25 TYR 0.038 0.002 TYR h 83 ARG 0.007 0.001 ARG c 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 103 average time/residue: 0.2827 time to fit residues: 42.2011 Evaluate side-chains 99 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1733 time to fit residues: 1.9036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.039244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.031777 restraints weight = 130981.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.032639 restraints weight = 71590.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.033238 restraints weight = 48927.575| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14386 Z= 0.232 Angle : 0.671 11.402 20853 Z= 0.385 Chirality : 0.036 0.190 2376 Planarity : 0.004 0.055 1478 Dihedral : 31.678 177.391 4581 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.29 % Allowed : 20.49 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.28), residues: 825 helix: 1.02 (0.21), residues: 586 sheet: -1.65 (1.53), residues: 10 loop : -0.42 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS f 75 PHE 0.009 0.001 PHE a 67 TYR 0.054 0.002 TYR h 83 ARG 0.006 0.000 ARG b 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2004.20 seconds wall clock time: 38 minutes 12.01 seconds (2292.01 seconds total)