Starting phenix.real_space_refine (version: dev) on Tue Feb 21 19:48:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/02_2023/7pf5_13368.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/02_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_13368/02_2023/7pf5_13368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/02_2023/7pf5_13368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/02_2023/7pf5_13368.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/02_2023/7pf5_13368.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "a PHE 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-dev-4877/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: 7.92, per 1000 atoms: 0.59 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: 7.58 Conformation dependent library (CDL) restraints added in 962.8 milliseconds 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: 5.85 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: 6.45 Time building geometry restraints manager: 8.01 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: 5861 35.82 - 71.64: 1618 71.64 - 107.45: 24 107.45 - 143.27: 1 143.27 - 179.09: 3 Dihedral angle restraints: 7507 sinusoidal: 5076 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 7504 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 7.090 Check model and map are aligned: 0.220 Process input model: 44.630 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 29.079 179.090 5941 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 % 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 *********************** 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 : 1.268 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3019 time to fit residues: 64.6832 Evaluate side-chains 96 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2891 ------------------------------------------------------------------------------- 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: 6.9990 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: 4.9990 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** ** 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: 0.8018 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 14386 Z= 0.216 Angle : 0.625 9.069 20853 Z= 0.367 Chirality : 0.035 0.161 2376 Planarity : 0.004 0.057 1478 Dihedral : 32.259 179.126 4289 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 0.72 % 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: 0.70 (0.27), residues: 825 helix: 0.92 (0.20), residues: 586 sheet: -0.46 (1.85), residues: 10 loop : -0.47 (0.36), residues: 229 *********************** 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 126 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 125 average time/residue: 0.2601 time to fit residues: 47.2768 Evaluate side-chains 96 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1199 time to fit residues: 2.0862 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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: 0.8109 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 14386 Z= 0.297 Angle : 0.637 9.749 20853 Z= 0.373 Chirality : 0.035 0.156 2376 Planarity : 0.004 0.055 1478 Dihedral : 32.283 175.085 4289 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 1.44 % 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: 1.01 (0.28), residues: 825 helix: 1.17 (0.21), residues: 588 sheet: -0.58 (1.93), residues: 10 loop : -0.42 (0.37), residues: 227 *********************** 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 117 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 112 average time/residue: 0.3005 time to fit residues: 49.3845 Evaluate side-chains 98 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1276 time to fit residues: 3.1610 ------------------------------------------------------------------------------- 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: 5.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** u 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 14386 Z= 0.329 Angle : 0.657 11.103 20853 Z= 0.382 Chirality : 0.036 0.177 2376 Planarity : 0.004 0.057 1478 Dihedral : 32.534 176.137 4289 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 1.15 % 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: 1.03 (0.28), residues: 825 helix: 1.22 (0.21), residues: 584 sheet: -0.56 (2.02), residues: 10 loop : -0.51 (0.37), residues: 231 *********************** 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 114 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 111 average time/residue: 0.2991 time to fit residues: 46.9152 Evaluate side-chains 94 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1245 time to fit residues: 1.9298 ------------------------------------------------------------------------------- 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: 0.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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** g 104 GLN ** 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: 0.8199 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 14386 Z= 0.349 Angle : 0.676 11.239 20853 Z= 0.391 Chirality : 0.037 0.215 2376 Planarity : 0.004 0.055 1478 Dihedral : 32.720 176.535 4289 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 1.88 % 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: 0.83 (0.28), residues: 825 helix: 1.04 (0.21), residues: 586 sheet: -0.69 (1.97), residues: 10 loop : -0.48 (0.36), residues: 229 *********************** 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 119 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 109 average time/residue: 0.2930 time to fit residues: 45.4489 Evaluate side-chains 101 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1360 time to fit residues: 3.0624 ------------------------------------------------------------------------------- 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: 0.1980 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.0070 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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** h 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 14386 Z= 0.190 Angle : 0.626 11.545 20853 Z= 0.360 Chirality : 0.035 0.184 2376 Planarity : 0.004 0.057 1478 Dihedral : 32.318 177.091 4289 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 1.01 % 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: 1.23 (0.28), residues: 825 helix: 1.37 (0.21), residues: 584 sheet: -0.95 (1.74), residues: 10 loop : -0.40 (0.38), residues: 231 *********************** 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 132 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 128 average time/residue: 0.2883 time to fit residues: 52.7394 Evaluate side-chains 105 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1381 time to fit residues: 2.1662 ------------------------------------------------------------------------------- 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: 0.7980 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.8149 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 14386 Z= 0.273 Angle : 0.639 11.437 20853 Z= 0.370 Chirality : 0.035 0.230 2376 Planarity : 0.004 0.056 1478 Dihedral : 32.419 177.252 4289 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.15 % 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: 1.12 (0.28), residues: 825 helix: 1.28 (0.21), residues: 582 sheet: -1.00 (1.74), residues: 10 loop : -0.40 (0.37), residues: 233 *********************** 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 119 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 115 average time/residue: 0.2821 time to fit residues: 46.3508 Evaluate side-chains 105 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1215 time to fit residues: 2.5700 ------------------------------------------------------------------------------- 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: 1.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 14386 Z= 0.413 Angle : 0.724 11.961 20853 Z= 0.413 Chirality : 0.038 0.186 2376 Planarity : 0.005 0.056 1478 Dihedral : 32.783 177.332 4289 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.15 % 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: 0.58 (0.28), residues: 825 helix: 0.85 (0.21), residues: 582 sheet: -1.31 (1.83), residues: 10 loop : -0.52 (0.37), residues: 233 *********************** 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 106 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 102 average time/residue: 0.3006 time to fit residues: 43.2740 Evaluate side-chains 95 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1258 time to fit residues: 1.7335 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 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 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** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5059 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= 0.239 Angle : 0.667 11.592 20853 Z= 0.380 Chirality : 0.036 0.192 2376 Planarity : 0.004 0.057 1478 Dihedral : 32.552 177.324 4289 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.43 % 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: 1.05 (0.21), residues: 584 sheet: -1.30 (1.71), residues: 10 loop : -0.53 (0.38), residues: 231 *********************** 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 113 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 110 average time/residue: 0.2672 time to fit residues: 42.8226 Evaluate side-chains 97 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1703 time to fit residues: 1.6285 ------------------------------------------------------------------------------- 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: 0.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 14386 Z= 0.240 Angle : 0.659 11.877 20853 Z= 0.378 Chirality : 0.036 0.253 2376 Planarity : 0.004 0.057 1478 Dihedral : 32.441 177.807 4289 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.29 % 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: 0.71 (0.28), residues: 825 helix: 0.96 (0.21), residues: 584 sheet: -1.26 (1.68), residues: 10 loop : -0.51 (0.38), residues: 231 ********************** 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 109 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 107 average time/residue: 0.2782 time to fit residues: 43.1351 Evaluate side-chains 102 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1632 time to fit residues: 1.7912 ------------------------------------------------------------------------------- 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: 0.9980 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.040270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.032829 restraints weight = 128238.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.033695 restraints weight = 71220.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.034303 restraints weight = 49190.426| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5374 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= 0.208 Angle : 0.654 11.510 20853 Z= 0.372 Chirality : 0.035 0.193 2376 Planarity : 0.004 0.059 1478 Dihedral : 32.195 177.507 4289 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.29 % 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: 0.77 (0.28), residues: 825 helix: 1.01 (0.21), residues: 584 sheet: -1.31 (1.63), residues: 10 loop : -0.49 (0.38), residues: 231 =============================================================================== Job complete usr+sys time: 1877.03 seconds wall clock time: 35 minutes 19.99 seconds (2119.99 seconds total)