Starting phenix.real_space_refine on Thu Jan 18 22:59:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/01_2024/8gi1_40059.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/01_2024/8gi1_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_40059/01_2024/8gi1_40059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/01_2024/8gi1_40059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/01_2024/8gi1_40059.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/01_2024/8gi1_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-1.21-5211/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: 5.44, 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: 3.87 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: 0.96 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: 2.59 Time building geometry restraints manager: 4.11 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: 0.580 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: 0.020 Extract box with map and model: 2.740 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.870 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- 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 : 1.138 Fit side-chains REVERT: B 112 MET cc_start: 0.8371 (ptm) cc_final: 0.8033 (ptm) REVERT: C 56 LYS cc_start: 0.8538 (pttt) cc_final: 0.8319 (pttp) REVERT: D 53 SER cc_start: 0.8369 (m) cc_final: 0.8022 (p) REVERT: D 112 MET cc_start: 0.8362 (ptm) cc_final: 0.8010 (ptm) REVERT: E 56 LYS cc_start: 0.8546 (pttt) cc_final: 0.8314 (pttp) REVERT: F 112 MET cc_start: 0.8400 (ptm) cc_final: 0.8024 (ptm) REVERT: G 56 LYS cc_start: 0.8562 (pttt) cc_final: 0.8251 (pttp) REVERT: H 53 SER cc_start: 0.8361 (m) cc_final: 0.8036 (p) REVERT: H 112 MET cc_start: 0.8340 (ptm) cc_final: 0.8029 (ptm) outliers start: 9 outliers final: 8 residues processed: 277 average time/residue: 0.2345 time to fit residues: 87.2898 Evaluate side-chains 126 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain E residue 85 TYR Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain H residue 85 TYR 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: 1.9990 chunk 28 optimal weight: 40.0000 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 101 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 91 ASN C 30 GLN C 91 ASN E 91 ASN G 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.3526 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= 0.226 Angle : 0.592 10.859 13240 Z= 0.330 Chirality : 0.038 0.192 1432 Planarity : 0.003 0.024 1656 Dihedral : 4.914 41.594 1312 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.96 % Allowed : 13.17 % Favored : 83.87 % 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: 3.38 (0.25), residues: 1120 helix: 3.02 (0.18), residues: 720 sheet: None (None), residues: 0 loop : 0.84 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 73 HIS 0.003 0.001 HIS B 32 PHE 0.010 0.002 PHE H 130 TYR 0.022 0.002 TYR A 24 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 194 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.229 Fit side-chains REVERT: A 102 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7550 (mt-10) REVERT: A 124 ARG cc_start: 0.7598 (ttt-90) cc_final: 0.7348 (tmt170) REVERT: B 90 GLU cc_start: 0.6206 (mm-30) cc_final: 0.5822 (pp20) REVERT: C 40 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6715 (tm-30) REVERT: C 56 LYS cc_start: 0.8874 (pttt) cc_final: 0.8488 (pttp) REVERT: C 90 GLU cc_start: 0.6458 (mm-30) cc_final: 0.5858 (pp20) REVERT: C 102 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7386 (mt-10) REVERT: C 124 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.7245 (tmt170) REVERT: D 90 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5647 (pp20) REVERT: E 56 LYS cc_start: 0.8873 (pttt) cc_final: 0.8484 (pttp) REVERT: E 90 GLU cc_start: 0.6634 (mm-30) cc_final: 0.5893 (pp20) REVERT: E 102 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7250 (mt-10) REVERT: E 124 ARG cc_start: 0.7480 (ttt-90) cc_final: 0.7237 (tmt170) REVERT: F 40 GLU cc_start: 0.6985 (tm-30) cc_final: 0.6312 (tm-30) REVERT: F 90 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5631 (pp20) REVERT: G 56 LYS cc_start: 0.8884 (pttt) cc_final: 0.8490 (pttp) REVERT: G 102 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7365 (mt-10) REVERT: G 124 ARG cc_start: 0.7526 (ttt-90) cc_final: 0.7237 (tmt170) REVERT: H 90 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5646 (pp20) REVERT: H 122 GLU cc_start: 0.6641 (tt0) cc_final: 0.6408 (tt0) outliers start: 31 outliers final: 17 residues processed: 181 average time/residue: 0.2486 time to fit residues: 60.3336 Evaluate side-chains 140 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 TYR Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain H residue 72 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 50.0000 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 40.0000 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 100 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4151 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= 0.188 Angle : 0.505 7.050 13240 Z= 0.284 Chirality : 0.035 0.174 1432 Planarity : 0.003 0.025 1656 Dihedral : 4.108 37.594 1304 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.15 % Allowed : 14.03 % Favored : 82.82 % 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: 2.98 (0.25), residues: 1120 helix: 3.22 (0.19), residues: 632 sheet: None (None), residues: 0 loop : 0.31 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 73 HIS 0.002 0.001 HIS G 157 PHE 0.006 0.001 PHE C 95 TYR 0.018 0.001 TYR C 24 ARG 0.005 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 191 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 1.157 Fit side-chains REVERT: A 63 ASN cc_start: 0.6798 (p0) cc_final: 0.6462 (p0) REVERT: A 124 ARG cc_start: 0.7523 (ttt-90) cc_final: 0.7322 (tmt170) REVERT: A 135 GLN cc_start: 0.5822 (tp40) cc_final: 0.5202 (pp30) REVERT: B 90 GLU cc_start: 0.6213 (mm-30) cc_final: 0.5905 (pp20) REVERT: B 112 MET cc_start: 0.7837 (ptm) cc_final: 0.7623 (ptm) REVERT: C 56 LYS cc_start: 0.8863 (pttt) cc_final: 0.8487 (pttp) REVERT: C 102 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7351 (mt-10) REVERT: C 124 ARG cc_start: 0.7482 (ttt-90) cc_final: 0.7245 (tmt170) REVERT: C 135 GLN cc_start: 0.5838 (tp40) cc_final: 0.5205 (pp30) REVERT: D 90 GLU cc_start: 0.6559 (mm-30) cc_final: 0.5784 (pp20) REVERT: D 112 MET cc_start: 0.7839 (ptm) cc_final: 0.7598 (ptm) REVERT: E 56 LYS cc_start: 0.8837 (pttt) cc_final: 0.8439 (pttp) REVERT: E 90 GLU cc_start: 0.6615 (mm-30) cc_final: 0.5970 (pp20) REVERT: E 102 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7317 (mt-10) REVERT: E 124 ARG cc_start: 0.7418 (ttt-90) cc_final: 0.7195 (tmt170) REVERT: E 135 GLN cc_start: 0.5844 (tp40) cc_final: 0.5212 (pp30) REVERT: F 40 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6383 (tm-30) REVERT: F 90 GLU cc_start: 0.6577 (mm-30) cc_final: 0.5750 (pp20) REVERT: F 112 MET cc_start: 0.7864 (ptm) cc_final: 0.7616 (ptm) REVERT: G 56 LYS cc_start: 0.8852 (pttt) cc_final: 0.8481 (pttp) REVERT: G 102 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7286 (mt-10) REVERT: G 124 ARG cc_start: 0.7418 (ttt-90) cc_final: 0.7154 (tmt170) REVERT: G 135 GLN cc_start: 0.5812 (tp40) cc_final: 0.5192 (pp30) REVERT: G 143 ARG cc_start: 0.7425 (ttm110) cc_final: 0.7125 (ttp-110) REVERT: H 90 GLU cc_start: 0.6518 (mm-30) cc_final: 0.5762 (pp20) REVERT: H 112 MET cc_start: 0.7820 (ptm) cc_final: 0.7568 (ptm) outliers start: 33 outliers final: 18 residues processed: 182 average time/residue: 0.2573 time to fit residues: 62.4101 Evaluate side-chains 137 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 TYR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 164 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 0.0970 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 51 HIS G 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9872 Z= 0.149 Angle : 0.458 5.395 13240 Z= 0.259 Chirality : 0.034 0.144 1432 Planarity : 0.003 0.027 1656 Dihedral : 4.044 41.221 1304 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.96 % Allowed : 15.08 % Favored : 81.97 % 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: 2.84 (0.25), residues: 1120 helix: 3.25 (0.19), residues: 632 sheet: None (None), residues: 0 loop : 0.02 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP E 73 HIS 0.002 0.001 HIS B 32 PHE 0.006 0.001 PHE G 87 TYR 0.017 0.001 TYR F 26 ARG 0.006 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 171 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 63 ASN cc_start: 0.7278 (p0) cc_final: 0.6987 (p0) REVERT: A 135 GLN cc_start: 0.5864 (tp40) cc_final: 0.5581 (pp30) REVERT: B 90 GLU cc_start: 0.6504 (mm-30) cc_final: 0.6082 (pp20) REVERT: C 56 LYS cc_start: 0.8819 (pttt) cc_final: 0.8601 (pttp) REVERT: C 135 GLN cc_start: 0.5901 (tp40) cc_final: 0.5574 (pp30) REVERT: C 143 ARG cc_start: 0.7424 (ttm110) cc_final: 0.7120 (ttp-110) REVERT: D 90 GLU cc_start: 0.6695 (mm-30) cc_final: 0.5851 (pp20) REVERT: D 135 GLN cc_start: 0.5198 (tp40) cc_final: 0.4579 (pp30) REVERT: E 56 LYS cc_start: 0.8803 (pttt) cc_final: 0.8564 (pttp) REVERT: E 63 ASN cc_start: 0.7374 (p0) cc_final: 0.7085 (p0) REVERT: E 135 GLN cc_start: 0.5794 (tp40) cc_final: 0.5477 (pp30) REVERT: F 56 LYS cc_start: 0.8826 (pttt) cc_final: 0.8580 (pttp) REVERT: F 90 GLU cc_start: 0.6697 (mm-30) cc_final: 0.5825 (pp20) REVERT: F 102 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6612 (mt-10) REVERT: G 56 LYS cc_start: 0.8815 (pttt) cc_final: 0.8595 (pttp) REVERT: G 135 GLN cc_start: 0.5851 (tp40) cc_final: 0.5538 (pp30) REVERT: G 143 ARG cc_start: 0.7443 (ttm110) cc_final: 0.7182 (ttp-110) REVERT: H 90 GLU cc_start: 0.6558 (mm-30) cc_final: 0.5834 (pp20) REVERT: H 135 GLN cc_start: 0.5180 (tp40) cc_final: 0.4564 (pp30) outliers start: 31 outliers final: 16 residues processed: 163 average time/residue: 0.2552 time to fit residues: 55.9835 Evaluate side-chains 137 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 TYR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 164 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 55 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS C 51 HIS D 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9872 Z= 0.197 Angle : 0.493 9.631 13240 Z= 0.275 Chirality : 0.035 0.136 1432 Planarity : 0.003 0.026 1656 Dihedral : 4.053 37.581 1304 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.96 % Allowed : 15.08 % Favored : 81.97 % 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 (0.25), residues: 1120 helix: 3.27 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.34 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 73 HIS 0.002 0.001 HIS A 51 PHE 0.005 0.001 PHE G 95 TYR 0.016 0.001 TYR F 26 ARG 0.006 0.000 ARG D 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 157 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7080 (tm-30) REVERT: A 63 ASN cc_start: 0.7264 (p0) cc_final: 0.7021 (p0) REVERT: B 90 GLU cc_start: 0.6822 (mm-30) cc_final: 0.5922 (pp20) REVERT: C 56 LYS cc_start: 0.8857 (pttt) cc_final: 0.8509 (pttp) REVERT: C 63 ASN cc_start: 0.7305 (p0) cc_final: 0.7040 (p0) REVERT: C 102 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7378 (mt-10) REVERT: C 124 ARG cc_start: 0.7583 (ttt-90) cc_final: 0.7268 (tmt170) REVERT: C 135 GLN cc_start: 0.5759 (tp40) cc_final: 0.5529 (pp30) REVERT: D 135 GLN cc_start: 0.5625 (tp40) cc_final: 0.4927 (pp30) REVERT: E 56 LYS cc_start: 0.8831 (pttt) cc_final: 0.8572 (pttp) REVERT: E 63 ASN cc_start: 0.7304 (p0) cc_final: 0.7025 (p0) REVERT: F 56 LYS cc_start: 0.8688 (pttt) cc_final: 0.8296 (pttm) REVERT: F 112 MET cc_start: 0.8042 (ptm) cc_final: 0.7689 (ptm) REVERT: G 56 LYS cc_start: 0.8858 (pttt) cc_final: 0.8500 (pttp) REVERT: G 63 ASN cc_start: 0.7370 (p0) cc_final: 0.7110 (p0) REVERT: G 102 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7350 (mt-10) REVERT: H 135 GLN cc_start: 0.5615 (tp40) cc_final: 0.4907 (pp30) outliers start: 31 outliers final: 21 residues processed: 148 average time/residue: 0.2638 time to fit residues: 52.8044 Evaluate side-chains 149 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 TYR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 164 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.2233 > 50: distance: 28 - 32: 21.634 distance: 32 - 33: 25.934 distance: 33 - 34: 47.396 distance: 33 - 36: 13.113 distance: 36 - 37: 59.820 distance: 37 - 38: 21.814 distance: 37 - 39: 17.435 distance: 40 - 41: 27.199 distance: 41 - 42: 12.916 distance: 41 - 44: 27.887 distance: 42 - 46: 20.641 distance: 44 - 45: 40.718 distance: 46 - 47: 32.474 distance: 47 - 48: 44.172 distance: 47 - 50: 16.478 distance: 48 - 49: 18.001 distance: 48 - 54: 9.198 distance: 50 - 52: 11.222 distance: 54 - 55: 6.309 distance: 55 - 56: 8.270 distance: 55 - 58: 26.019 distance: 56 - 57: 47.223 distance: 56 - 62: 21.081 distance: 58 - 59: 22.873 distance: 59 - 60: 28.001 distance: 59 - 61: 28.018 distance: 62 - 63: 16.725 distance: 62 - 129: 24.621 distance: 63 - 64: 40.178 distance: 63 - 66: 24.660 distance: 64 - 65: 31.918 distance: 64 - 70: 6.748 distance: 65 - 126: 24.134 distance: 66 - 67: 14.177 distance: 66 - 68: 39.217 distance: 67 - 69: 15.122 distance: 70 - 71: 5.957 distance: 71 - 72: 14.184 distance: 71 - 74: 13.452 distance: 72 - 84: 15.814 distance: 74 - 75: 22.975 distance: 75 - 76: 15.638 distance: 75 - 77: 6.797 distance: 76 - 78: 16.565 distance: 77 - 79: 11.578 distance: 77 - 80: 11.964 distance: 78 - 79: 11.794 distance: 79 - 81: 11.729 distance: 80 - 82: 16.161 distance: 81 - 83: 6.916 distance: 82 - 83: 15.694 distance: 84 - 85: 21.592 distance: 85 - 86: 14.813 distance: 85 - 88: 6.704 distance: 86 - 93: 7.011 distance: 88 - 89: 18.857 distance: 89 - 90: 8.800 distance: 90 - 91: 4.665 distance: 90 - 92: 11.550 distance: 93 - 94: 13.531 distance: 94 - 95: 18.620 distance: 94 - 97: 12.578 distance: 95 - 96: 18.069 distance: 97 - 98: 5.936 distance: 98 - 99: 21.547 distance: 99 - 100: 28.953 distance: 100 - 101: 22.341 distance: 102 - 103: 23.587 distance: 103 - 104: 15.126 distance: 103 - 106: 47.268 distance: 104 - 105: 13.651 distance: 106 - 107: 10.843 distance: 107 - 108: 22.983 distance: 107 - 109: 27.282 distance: 108 - 110: 23.367 distance: 110 - 112: 34.939 distance: 111 - 112: 22.768 distance: 112 - 113: 28.000 distance: 114 - 115: 40.180 distance: 115 - 116: 7.347 distance: 115 - 118: 4.613 distance: 116 - 117: 3.695 distance: 116 - 126: 28.747 distance: 118 - 119: 9.986 distance: 119 - 120: 6.922 distance: 119 - 121: 51.168 distance: 120 - 122: 36.882 distance: 122 - 124: 25.958 distance: 123 - 124: 43.770