Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 09:43:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v90_31806/04_2023/7v90_31806.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v90_31806/04_2023/7v90_31806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v90_31806/04_2023/7v90_31806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v90_31806/04_2023/7v90_31806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v90_31806/04_2023/7v90_31806.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v90_31806/04_2023/7v90_31806.pdb" } resolution = 3.5 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 14 5.16 5 C 6737 2.51 5 N 2288 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12148 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 824 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} 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: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} 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: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 3067 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2872 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 6.90, per 1000 atoms: 0.57 Number of scatterers: 12148 At special positions: 0 Unit cell: (115.83, 113.256, 124.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 288 15.00 O 2821 8.00 N 2288 7.00 C 6737 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: 6.28 Conformation dependent library (CDL) restraints added in 1.2 seconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1458 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 69.4% alpha, 2.3% beta 123 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 5.20 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 64 through 75 removed outlier: 3.633A pdb=" N ALA A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.575A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.977A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 126' Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.568A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.796A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.794A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 94 " --> pdb=" O LEU B 90 " (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: 4.467A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 95 removed outlier: 4.057A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.699A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.566A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.667A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.745A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.644A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 76 Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.680A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.577A 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 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.597A pdb=" N LYS H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.759A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.720A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.004A 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 'B' and resid 96 through 98 removed outlier: 6.447A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (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: 7.439A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 removed outlier: 7.007A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.102A 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 'G' and resid 42 through 43 removed outlier: 7.665A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 380 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 306 hydrogen bonds 612 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1411 1.32 - 1.44: 4779 1.44 - 1.56: 6161 1.56 - 1.69: 576 1.69 - 1.81: 24 Bond restraints: 12951 Sorted by residual: bond pdb=" N ASP C 90 " pdb=" CA ASP C 90 " ideal model delta sigma weight residual 1.456 1.529 -0.074 1.25e-02 6.40e+03 3.47e+01 bond pdb=" CA SER D 35 " pdb=" CB SER D 35 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.58e-02 4.01e+03 1.19e+01 bond pdb=" O3' DG I 12 " pdb=" P DG I 13 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" O3' DG I -66 " pdb=" P DG I -65 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 1.00e+01 bond pdb=" N ARG A 129 " pdb=" CA ARG A 129 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 9.90e+00 ... (remaining 12946 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.30: 1237 105.30 - 112.10: 7101 112.10 - 118.90: 3503 118.90 - 125.71: 5895 125.71 - 132.51: 982 Bond angle restraints: 18718 Sorted by residual: angle pdb=" C TYR D 34 " pdb=" CA TYR D 34 " pdb=" CB TYR D 34 " ideal model delta sigma weight residual 112.12 103.64 8.48 1.50e+00 4.44e-01 3.20e+01 angle pdb=" N LEU A 126 " pdb=" CA LEU A 126 " pdb=" C LEU A 126 " ideal model delta sigma weight residual 112.87 106.38 6.49 1.20e+00 6.94e-01 2.92e+01 angle pdb=" N ARG A 128 " pdb=" CA ARG A 128 " pdb=" C ARG A 128 " ideal model delta sigma weight residual 110.80 99.99 10.81 2.13e+00 2.20e-01 2.58e+01 angle pdb=" N ASP C 90 " pdb=" CA ASP C 90 " pdb=" C ASP C 90 " ideal model delta sigma weight residual 110.35 117.18 -6.83 1.36e+00 5.41e-01 2.52e+01 angle pdb=" N PHE F 100 " pdb=" CA PHE F 100 " pdb=" C PHE F 100 " ideal model delta sigma weight residual 113.18 107.27 5.91 1.21e+00 6.83e-01 2.38e+01 ... (remaining 18713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.87: 5398 30.87 - 61.74: 1394 61.74 - 92.61: 24 92.61 - 123.48: 0 123.48 - 154.35: 1 Dihedral angle restraints: 6817 sinusoidal: 4556 harmonic: 2261 Sorted by residual: dihedral pdb=" N ASP C 90 " pdb=" C ASP C 90 " pdb=" CA ASP C 90 " pdb=" CB ASP C 90 " ideal model delta harmonic sigma weight residual 122.80 135.60 -12.80 0 2.50e+00 1.60e-01 2.62e+01 dihedral pdb=" C ASP C 90 " pdb=" N ASP C 90 " pdb=" CA ASP C 90 " pdb=" CB ASP C 90 " ideal model delta harmonic sigma weight residual -122.60 -133.28 10.68 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C ARG C 20 " pdb=" N ARG C 20 " pdb=" CA ARG C 20 " pdb=" CB ARG C 20 " ideal model delta harmonic sigma weight residual -122.60 -133.22 10.62 0 2.50e+00 1.60e-01 1.81e+01 ... (remaining 6814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1989 0.080 - 0.160: 110 0.160 - 0.240: 16 0.240 - 0.320: 7 0.320 - 0.400: 1 Chirality restraints: 2123 Sorted by residual: chirality pdb=" CA ASP C 90 " pdb=" N ASP C 90 " pdb=" C ASP C 90 " pdb=" CB ASP C 90 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA TYR D 34 " pdb=" N TYR D 34 " pdb=" C TYR D 34 " pdb=" CB TYR D 34 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ARG C 20 " pdb=" N ARG C 20 " pdb=" C ARG C 20 " pdb=" CB ARG C 20 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 2120 not shown) Planarity restraints: 1365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 90 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C ASP C 90 " -0.060 2.00e-02 2.50e+03 pdb=" O ASP C 90 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU C 91 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 88 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ARG C 88 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG C 88 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN C 89 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 125 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C GLN A 125 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN A 125 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 126 " 0.009 2.00e-02 2.50e+03 ... (remaining 1362 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1458 2.75 - 3.29: 10271 3.29 - 3.83: 22498 3.83 - 4.36: 25965 4.36 - 4.90: 39112 Nonbonded interactions: 99304 Sorted by model distance: nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.219 2.440 nonbonded pdb=" O GLU D 102 " pdb=" ND1 HIS D 106 " model vdw 2.303 2.520 nonbonded pdb=" O ILE A 119 " pdb=" OG SER B 47 " model vdw 2.398 2.440 nonbonded pdb=" N2 DG I -28 " pdb=" N3 DC J 28 " model vdw 2.416 2.600 nonbonded pdb=" NH1 ARG G 32 " pdb=" OP1 DC J -44 " model vdw 2.430 2.520 ... (remaining 99299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 36 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 24 through 121) 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.720 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 39.330 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.005 0.074 12951 Z= 0.296 Angle : 0.727 10.814 18718 Z= 0.489 Chirality : 0.044 0.400 2123 Planarity : 0.003 0.035 1365 Dihedral : 26.190 154.348 5359 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.71 % Favored : 94.77 % Rotamer Outliers : 4.01 % Cbeta Deviations : 0.41 % 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: -0.16 (0.28), residues: 765 helix: 0.89 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.20 (0.30), residues: 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 5 residues processed: 141 average time/residue: 0.4558 time to fit residues: 78.8675 Evaluate side-chains 66 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2578 time to fit residues: 2.9233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 84 GLN D 44 GLN D 60 ASN G 84 GLN H 46 HIS H 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 12951 Z= 0.194 Angle : 0.551 6.689 18718 Z= 0.329 Chirality : 0.033 0.169 2123 Planarity : 0.004 0.040 1365 Dihedral : 30.596 159.686 3789 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.14 % Favored : 96.60 % Rotamer Outliers : 1.08 % 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: 1.38 (0.29), residues: 765 helix: 2.05 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.87 (0.33), residues: 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 1.007 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.3203 time to fit residues: 37.0873 Evaluate side-chains 70 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1043 time to fit residues: 2.3253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 63 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS E 68 GLN F 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 12951 Z= 0.232 Angle : 0.557 7.120 18718 Z= 0.332 Chirality : 0.034 0.156 2123 Planarity : 0.004 0.047 1365 Dihedral : 30.529 162.799 3789 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.05 % Favored : 95.69 % Rotamer Outliers : 1.54 % 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: 1.71 (0.30), residues: 765 helix: 2.29 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.907 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 86 average time/residue: 0.3233 time to fit residues: 37.5486 Evaluate side-chains 70 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2078 time to fit residues: 2.6834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.0030 chunk 44 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 12951 Z= 0.147 Angle : 0.489 5.811 18718 Z= 0.298 Chirality : 0.031 0.181 2123 Planarity : 0.003 0.033 1365 Dihedral : 30.399 162.635 3789 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.27 % Favored : 96.60 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.31), residues: 765 helix: 2.83 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.52 (0.36), residues: 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.960 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 77 average time/residue: 0.2766 time to fit residues: 30.3443 Evaluate side-chains 64 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1096 time to fit residues: 1.4627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12951 Z= 0.190 Angle : 0.510 5.276 18718 Z= 0.308 Chirality : 0.032 0.163 2123 Planarity : 0.004 0.032 1365 Dihedral : 30.434 162.626 3789 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.31), residues: 765 helix: 2.81 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.48 (0.36), residues: 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.873 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 72 average time/residue: 0.3051 time to fit residues: 30.3868 Evaluate side-chains 73 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1131 time to fit residues: 3.1153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.1980 chunk 8 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12951 Z= 0.152 Angle : 0.485 5.000 18718 Z= 0.296 Chirality : 0.031 0.147 2123 Planarity : 0.003 0.031 1365 Dihedral : 30.349 162.624 3789 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.75 % Favored : 97.12 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.31), residues: 765 helix: 3.00 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.33 (0.37), residues: 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.981 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.2978 time to fit residues: 29.7594 Evaluate side-chains 65 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1236 time to fit residues: 1.6136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12951 Z= 0.180 Angle : 0.503 6.174 18718 Z= 0.304 Chirality : 0.032 0.147 2123 Planarity : 0.003 0.031 1365 Dihedral : 30.412 162.741 3789 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.31), residues: 765 helix: 2.97 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.20 (0.37), residues: 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.996 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 70 average time/residue: 0.3346 time to fit residues: 31.6830 Evaluate side-chains 70 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1991 time to fit residues: 2.9933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 12951 Z= 0.233 Angle : 0.544 8.340 18718 Z= 0.326 Chirality : 0.034 0.161 2123 Planarity : 0.004 0.052 1365 Dihedral : 30.536 163.292 3789 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.53 % Favored : 96.34 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.31), residues: 765 helix: 2.72 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.36 (0.36), residues: 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 1.052 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.3443 time to fit residues: 33.8993 Evaluate side-chains 68 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1033 time to fit residues: 1.5970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 12951 Z= 0.271 Angle : 0.571 8.609 18718 Z= 0.340 Chirality : 0.036 0.162 2123 Planarity : 0.004 0.056 1365 Dihedral : 30.753 163.586 3789 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.97 % Favored : 94.90 % Rotamer Outliers : 0.77 % 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: 1.96 (0.30), residues: 765 helix: 2.48 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.57 (0.35), residues: 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 1.034 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.3589 time to fit residues: 33.8899 Evaluate side-chains 68 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1179 time to fit residues: 2.0265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 12951 Z= 0.272 Angle : 0.574 9.503 18718 Z= 0.341 Chirality : 0.036 0.167 2123 Planarity : 0.004 0.054 1365 Dihedral : 30.774 163.689 3789 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 0.31 % 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: 1.83 (0.30), residues: 765 helix: 2.44 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.77 (0.34), residues: 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 1.086 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 69 average time/residue: 0.3377 time to fit residues: 31.5398 Evaluate side-chains 68 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1101 time to fit residues: 1.7292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 10 optimal weight: 0.0020 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.168372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125609 restraints weight = 14676.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124704 restraints weight = 33436.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.125819 restraints weight = 33073.245| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12951 Z= 0.160 Angle : 0.509 7.447 18718 Z= 0.309 Chirality : 0.032 0.184 2123 Planarity : 0.003 0.032 1365 Dihedral : 30.634 163.308 3789 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.15 % 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: 2.43 (0.31), residues: 765 helix: 2.91 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.55 (0.35), residues: 240 =============================================================================== Job complete usr+sys time: 1731.59 seconds wall clock time: 32 minutes 32.75 seconds (1952.75 seconds total)