Starting phenix.real_space_refine on Sat Dec 9 01:49:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/12_2023/8gi1_40059.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/12_2023/8gi1_40059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/12_2023/8gi1_40059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/12_2023/8gi1_40059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/12_2023/8gi1_40059.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/12_2023/8gi1_40059.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 6232 2.51 5 N 1664 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9704 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "B" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "C" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "D" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "E" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "F" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "G" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "H" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Time building chain proxies: 5.45, per 1000 atoms: 0.56 Number of scatterers: 9704 At special positions: 0 Unit cell: (121.03, 121.03, 91.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1776 8.00 N 1664 7.00 C 6232 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: 4.37 Conformation dependent library (CDL) restraints added in 1.8 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 75.8% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 19 through 56 removed outlier: 3.597A pdb=" N HIS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 91 through 104 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 113 through 135 Processing helix chain 'A' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'B' and resid 20 through 56 removed outlier: 3.691A pdb=" N TYR B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 25 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 36 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 91 through 104 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 113 through 135 Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'C' and resid 20 through 56 removed outlier: 3.597A pdb=" N HIS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 36 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 91 through 104 Processing helix chain 'C' and resid 107 through 111 Processing helix chain 'C' and resid 113 through 135 Processing helix chain 'C' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'D' and resid 20 through 56 removed outlier: 3.591A pdb=" N HIS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS D 56 " --> pdb=" O LYS D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 91 through 104 Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'D' and resid 113 through 135 Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'E' and resid 20 through 56 removed outlier: 3.531A pdb=" N SER E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 36 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 91 through 104 Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'E' and resid 113 through 135 Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.066A pdb=" N VAL E 150 " --> pdb=" O ASN E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'F' and resid 20 through 56 removed outlier: 3.636A pdb=" N TYR F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 42 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS F 56 " --> pdb=" O LYS F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 Processing helix chain 'F' and resid 91 through 104 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 113 through 135 Processing helix chain 'F' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 169 No H-bonds generated for 'chain 'F' and resid 167 through 169' Processing helix chain 'G' and resid 20 through 56 removed outlier: 3.594A pdb=" N HIS G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS G 56 " --> pdb=" O LYS G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 91 through 104 Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'G' and resid 113 through 135 Processing helix chain 'G' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL G 150 " --> pdb=" O ASN G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 169 No H-bonds generated for 'chain 'G' and resid 167 through 169' Processing helix chain 'H' and resid 20 through 56 removed outlier: 3.769A pdb=" N ILE H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA H 42 " --> pdb=" O ASN H 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS H 56 " --> pdb=" O LYS H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 62 Processing helix chain 'H' and resid 91 through 104 Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 113 through 135 Processing helix chain 'H' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL H 150 " --> pdb=" O ASN H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AA7, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AA8, first strand: chain 'H' and resid 71 through 72 650 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1708 1.31 - 1.43: 2573 1.43 - 1.55: 5427 1.55 - 1.68: 108 1.68 - 1.80: 56 Bond restraints: 9872 Sorted by residual: bond pdb=" CA SER E 35 " pdb=" C SER E 35 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.30e-02 5.92e+03 2.38e+01 bond pdb=" C GLN H 33 " pdb=" O GLN H 33 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.17e-02 7.31e+03 1.58e+01 bond pdb=" C VAL E 36 " pdb=" O VAL E 36 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.17e-02 7.31e+03 1.46e+01 bond pdb=" CA HIS C 32 " pdb=" C HIS C 32 " ideal model delta sigma weight residual 1.524 1.474 0.049 1.32e-02 5.74e+03 1.40e+01 bond pdb=" CB ILE F 110 " pdb=" CG1 ILE F 110 " ideal model delta sigma weight residual 1.530 1.455 0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 9867 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.27: 127 106.27 - 113.22: 4942 113.22 - 120.18: 4506 120.18 - 127.13: 3616 127.13 - 134.08: 49 Bond angle restraints: 13240 Sorted by residual: angle pdb=" N ASN H 38 " pdb=" CA ASN H 38 " pdb=" C ASN H 38 " ideal model delta sigma weight residual 112.54 122.14 -9.60 1.22e+00 6.72e-01 6.19e+01 angle pdb=" N ASN E 38 " pdb=" CA ASN E 38 " pdb=" C ASN E 38 " ideal model delta sigma weight residual 111.36 119.30 -7.94 1.09e+00 8.42e-01 5.30e+01 angle pdb=" N ASN F 38 " pdb=" CA ASN F 38 " pdb=" C ASN F 38 " ideal model delta sigma weight residual 112.89 120.48 -7.59 1.24e+00 6.50e-01 3.75e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.14 117.53 -6.39 1.08e+00 8.57e-01 3.50e+01 angle pdb=" N GLN F 33 " pdb=" CA GLN F 33 " pdb=" C GLN F 33 " ideal model delta sigma weight residual 112.54 106.19 6.35 1.22e+00 6.72e-01 2.71e+01 ... (remaining 13235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 5725 16.00 - 31.99: 172 31.99 - 47.99: 102 47.99 - 63.99: 47 63.99 - 79.99: 2 Dihedral angle restraints: 6048 sinusoidal: 2560 harmonic: 3488 Sorted by residual: dihedral pdb=" N ASN H 38 " pdb=" C ASN H 38 " pdb=" CA ASN H 38 " pdb=" CB ASN H 38 " ideal model delta harmonic sigma weight residual 122.80 137.41 -14.61 0 2.50e+00 1.60e-01 3.41e+01 dihedral pdb=" C ASN H 38 " pdb=" N ASN H 38 " pdb=" CA ASN H 38 " pdb=" CB ASN H 38 " ideal model delta harmonic sigma weight residual -122.60 -137.10 14.50 0 2.50e+00 1.60e-01 3.36e+01 dihedral pdb=" N ASN F 38 " pdb=" C ASN F 38 " pdb=" CA ASN F 38 " pdb=" CB ASN F 38 " ideal model delta harmonic sigma weight residual 122.80 134.67 -11.87 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 6045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1201 0.129 - 0.257: 215 0.257 - 0.385: 11 0.385 - 0.514: 3 0.514 - 0.642: 2 Chirality restraints: 1432 Sorted by residual: chirality pdb=" CA ASN H 38 " pdb=" N ASN H 38 " pdb=" C ASN H 38 " pdb=" CB ASN H 38 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ASN F 38 " pdb=" N ASN F 38 " pdb=" C ASN F 38 " pdb=" CB ASN F 38 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA ASN E 38 " pdb=" N ASN E 38 " pdb=" C ASN E 38 " pdb=" CB ASN E 38 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 ... (remaining 1429 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F 32 " -0.020 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C HIS F 32 " 0.074 2.00e-02 2.50e+03 pdb=" O HIS F 32 " -0.029 2.00e-02 2.50e+03 pdb=" N GLN F 33 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 33 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C GLN A 33 " -0.068 2.00e-02 2.50e+03 pdb=" O GLN A 33 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS A 34 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 36 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C VAL E 36 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL E 36 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU E 37 " -0.020 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 15 2.02 - 2.74: 1375 2.74 - 3.46: 13854 3.46 - 4.18: 21954 4.18 - 4.90: 38622 Nonbonded interactions: 75820 Sorted by model distance: nonbonded pdb=" CB ALA A 27 " pdb=" OH TYR H 26 " model vdw 1.301 3.460 nonbonded pdb=" OH TYR F 26 " pdb=" CB ALA G 27 " model vdw 1.346 3.460 nonbonded pdb=" OH TYR C 26 " pdb=" CB ALA D 27 " model vdw 1.515 3.460 nonbonded pdb=" CE2 TYR B 26 " pdb=" NE2 GLN B 30 " model vdw 1.563 3.420 nonbonded pdb=" OH TYR B 26 " pdb=" CB ALA C 27 " model vdw 1.598 3.460 ... (remaining 75815 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.740 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.320 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 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 : 0.017 0.081 9872 Z= 1.091 Angle : 1.445 9.600 13240 Z= 0.965 Chirality : 0.096 0.642 1432 Planarity : 0.007 0.043 1656 Dihedral : 11.694 79.986 3792 Min Nonbonded Distance : 1.301 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.86 % Allowed : 3.72 % Favored : 95.42 % Cbeta Deviations : 1.06 % 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: 1.00 (0.24), residues: 1120 helix: 0.91 (0.17), residues: 744 sheet: None (None), residues: 0 loop : 0.42 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.004 TRP E 73 HIS 0.007 0.002 HIS E 51 PHE 0.032 0.006 PHE G 87 TYR 0.015 0.003 TYR E 44 ARG 0.007 0.001 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 268 time to evaluate : 1.152 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 277 average time/residue: 0.2378 time to fit residues: 88.9048 Evaluate side-chains 121 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1203 time to fit residues: 3.1527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 40.0000 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.0000 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN C 30 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN G 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9872 Z= 0.215 Angle : 0.582 10.817 13240 Z= 0.325 Chirality : 0.038 0.213 1432 Planarity : 0.003 0.024 1656 Dihedral : 3.897 16.270 1296 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.48 % Allowed : 14.31 % Favored : 83.21 % 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: 3.43 (0.25), residues: 1120 helix: 3.05 (0.18), residues: 720 sheet: None (None), residues: 0 loop : 0.88 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 73 HIS 0.004 0.001 HIS B 32 PHE 0.009 0.001 PHE H 130 TYR 0.020 0.002 TYR F 26 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.169 Fit side-chains outliers start: 26 outliers final: 11 residues processed: 179 average time/residue: 0.2548 time to fit residues: 61.3877 Evaluate side-chains 132 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0888 time to fit residues: 3.4771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 30.0000 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 40.0000 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 91 ASN B 30 GLN G 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9872 Z= 0.199 Angle : 0.515 7.290 13240 Z= 0.288 Chirality : 0.036 0.173 1432 Planarity : 0.003 0.026 1656 Dihedral : 3.541 16.804 1296 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.43 % Allowed : 15.84 % Favored : 82.73 % 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: 2.80 (0.25), residues: 1120 helix: 3.15 (0.19), residues: 632 sheet: None (None), residues: 0 loop : 0.11 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 73 HIS 0.003 0.001 HIS G 157 PHE 0.008 0.001 PHE C 87 TYR 0.017 0.001 TYR C 24 ARG 0.004 0.000 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.062 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 162 average time/residue: 0.2298 time to fit residues: 51.3002 Evaluate side-chains 113 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0908 time to fit residues: 2.5588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9872 Z= 0.179 Angle : 0.490 5.653 13240 Z= 0.275 Chirality : 0.035 0.148 1432 Planarity : 0.003 0.031 1656 Dihedral : 3.523 16.065 1296 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.34 % Allowed : 16.51 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.25), residues: 1120 helix: 3.25 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.17 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 73 HIS 0.002 0.001 HIS B 32 PHE 0.005 0.001 PHE E 130 TYR 0.017 0.001 TYR F 26 ARG 0.005 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 1.117 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 141 average time/residue: 0.2454 time to fit residues: 47.3869 Evaluate side-chains 111 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0875 time to fit residues: 3.0398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS D 32 HIS D 51 HIS H 51 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 9872 Z= 0.296 Angle : 0.573 4.633 13240 Z= 0.317 Chirality : 0.038 0.134 1432 Planarity : 0.003 0.024 1656 Dihedral : 3.755 16.736 1296 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.72 % Allowed : 17.37 % Favored : 80.92 % 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: 2.41 (0.24), residues: 1120 helix: 3.11 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.51 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 73 HIS 0.003 0.001 HIS A 51 PHE 0.007 0.001 PHE B 111 TYR 0.018 0.001 TYR C 86 ARG 0.007 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.136 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 128 average time/residue: 0.2661 time to fit residues: 46.1860 Evaluate side-chains 97 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0846 time to fit residues: 2.3873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 40.0000 chunk 104 optimal weight: 0.2980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS C 51 HIS E 51 HIS E 91 ASN G 51 HIS H 32 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9872 Z= 0.276 Angle : 0.564 9.211 13240 Z= 0.310 Chirality : 0.038 0.128 1432 Planarity : 0.003 0.034 1656 Dihedral : 3.773 16.524 1296 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.81 % Allowed : 19.37 % Favored : 78.82 % 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: 2.17 (0.24), residues: 1120 helix: 3.08 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.89 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP G 73 HIS 0.003 0.001 HIS A 157 PHE 0.006 0.001 PHE D 111 TYR 0.017 0.001 TYR C 86 ARG 0.007 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.176 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 112 average time/residue: 0.2645 time to fit residues: 40.1246 Evaluate side-chains 104 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0942 time to fit residues: 3.8820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN F 32 HIS F 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9872 Z= 0.219 Angle : 0.511 7.608 13240 Z= 0.284 Chirality : 0.036 0.121 1432 Planarity : 0.003 0.029 1656 Dihedral : 3.636 16.229 1296 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.24 % Allowed : 19.27 % Favored : 79.48 % 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: 2.24 (0.24), residues: 1120 helix: 3.21 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.97 (0.24), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP G 73 HIS 0.002 0.001 HIS A 157 PHE 0.005 0.001 PHE E 95 TYR 0.014 0.001 TYR F 26 ARG 0.007 0.000 ARG F 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.265 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 117 average time/residue: 0.2851 time to fit residues: 45.0427 Evaluate side-chains 105 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1032 time to fit residues: 2.6434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9872 Z= 0.161 Angle : 0.462 7.286 13240 Z= 0.258 Chirality : 0.035 0.120 1432 Planarity : 0.003 0.038 1656 Dihedral : 3.505 15.846 1296 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.24 % Allowed : 18.99 % Favored : 79.77 % 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: 2.48 (0.24), residues: 1120 helix: 3.42 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.89 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP G 73 HIS 0.002 0.001 HIS G 32 PHE 0.006 0.001 PHE C 87 TYR 0.014 0.001 TYR F 26 ARG 0.010 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 1.131 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 125 average time/residue: 0.2721 time to fit residues: 45.6455 Evaluate side-chains 112 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0957 time to fit residues: 2.9583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9872 Z= 0.213 Angle : 0.501 6.961 13240 Z= 0.277 Chirality : 0.036 0.187 1432 Planarity : 0.003 0.026 1656 Dihedral : 3.579 16.240 1296 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.67 % Allowed : 19.37 % Favored : 79.96 % 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: 2.34 (0.24), residues: 1120 helix: 3.30 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.95 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP G 73 HIS 0.003 0.001 HIS E 157 PHE 0.005 0.001 PHE E 95 TYR 0.017 0.001 TYR A 24 ARG 0.006 0.000 ARG F 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.101 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 119 average time/residue: 0.2780 time to fit residues: 44.0716 Evaluate side-chains 110 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0992 time to fit residues: 2.1050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9872 Z= 0.200 Angle : 0.491 6.815 13240 Z= 0.272 Chirality : 0.036 0.215 1432 Planarity : 0.003 0.026 1656 Dihedral : 3.587 16.487 1296 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.48 % Allowed : 19.94 % Favored : 79.58 % 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: 2.30 (0.24), residues: 1120 helix: 3.27 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.97 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP G 73 HIS 0.003 0.001 HIS E 157 PHE 0.006 0.001 PHE E 95 TYR 0.017 0.001 TYR A 24 ARG 0.006 0.000 ARG D 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.157 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 117 average time/residue: 0.2865 time to fit residues: 44.5372 Evaluate side-chains 109 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0859 time to fit residues: 1.9317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.177090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.131454 restraints weight = 10523.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130201 restraints weight = 8789.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.129654 restraints weight = 8549.030| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9872 Z= 0.218 Angle : 0.509 6.771 13240 Z= 0.281 Chirality : 0.037 0.190 1432 Planarity : 0.003 0.026 1656 Dihedral : 3.635 16.705 1296 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.38 % Allowed : 20.04 % Favored : 79.58 % 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: 2.23 (0.24), residues: 1120 helix: 3.22 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP G 73 HIS 0.003 0.001 HIS E 157 PHE 0.005 0.001 PHE F 95 TYR 0.017 0.001 TYR A 24 ARG 0.005 0.000 ARG H 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1878.22 seconds wall clock time: 35 minutes 22.69 seconds (2122.69 seconds total)