Starting phenix.real_space_refine on Sun Mar 10 19:22:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pke_17736/03_2024/8pke_17736.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pke_17736/03_2024/8pke_17736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pke_17736/03_2024/8pke_17736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pke_17736/03_2024/8pke_17736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pke_17736/03_2024/8pke_17736.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pke_17736/03_2024/8pke_17736.pdb" } resolution = 3.39 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= 0.002 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 6 5.16 5 C 2796 2.51 5 N 708 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 34": "NH1" <-> "NH2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "F" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 2.75, per 1000 atoms: 0.64 Number of scatterers: 4314 At special positions: 0 Unit cell: (78.09, 79.734, 45.21, 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 6 16.00 O 804 8.00 N 708 7.00 C 2796 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: 1.73 Conformation dependent library (CDL) restraints added in 766.9 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.715A pdb=" N MET A 13 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL B 16 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 13 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL C 16 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET C 13 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL D 16 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET D 13 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL E 16 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET E 13 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL F 16 " --> pdb=" O MET E 13 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS E 15 " --> pdb=" O VAL F 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 5.972A pdb=" N ALA A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA B 19 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA C 19 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA D 19 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA E 19 " --> pdb=" O ILE F 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.409A pdb=" N ALA A 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA C 25 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA D 25 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA E 25 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 31 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 62 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 73 Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 6.886A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER B 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR C 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR D 78 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER D 77 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR E 78 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER E 77 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR F 78 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 99 removed outlier: 6.534A pdb=" N VAL A 93 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR B 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE A 95 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASN B 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA A 97 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR C 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE B 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASN C 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA B 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 93 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR D 96 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE C 95 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASN D 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA C 97 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL D 93 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR E 96 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE D 95 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASN E 98 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA D 97 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL E 93 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR F 96 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE E 95 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASN F 98 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA E 97 " --> pdb=" O ASN F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 110 removed outlier: 9.074A pdb=" N THR A 106 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ALA B 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA A 108 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N THR B 106 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ALA C 109 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA B 108 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N THR C 106 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N ALA D 109 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA C 108 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N THR D 106 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ALA E 109 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA D 108 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N THR E 106 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ALA F 109 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA E 108 " --> pdb=" O ALA F 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 122 75 hydrogen bonds defined for protein. 225 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: 1.10 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 777 1.32 - 1.45: 1125 1.45 - 1.57: 2502 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 4416 Sorted by residual: bond pdb=" N SER F 85 " pdb=" CA SER F 85 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.10e-03 1.21e+04 1.41e+01 bond pdb=" N SER E 85 " pdb=" CA SER E 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.36e+01 bond pdb=" N SER C 85 " pdb=" CA SER C 85 " ideal model delta sigma weight residual 1.457 1.489 -0.033 9.10e-03 1.21e+04 1.30e+01 bond pdb=" N SER D 85 " pdb=" CA SER D 85 " ideal model delta sigma weight residual 1.457 1.489 -0.033 9.10e-03 1.21e+04 1.30e+01 bond pdb=" N SER B 85 " pdb=" CA SER B 85 " ideal model delta sigma weight residual 1.457 1.489 -0.032 9.10e-03 1.21e+04 1.26e+01 ... (remaining 4411 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.19: 231 107.19 - 113.95: 2425 113.95 - 120.71: 2089 120.71 - 127.48: 1207 127.48 - 134.24: 54 Bond angle restraints: 6006 Sorted by residual: angle pdb=" CA SER A 85 " pdb=" C SER A 85 " pdb=" N PRO A 86 " ideal model delta sigma weight residual 118.16 122.33 -4.17 7.00e-01 2.04e+00 3.55e+01 angle pdb=" CA SER F 85 " pdb=" C SER F 85 " pdb=" N PRO F 86 " ideal model delta sigma weight residual 118.16 122.32 -4.16 7.00e-01 2.04e+00 3.53e+01 angle pdb=" CA SER B 85 " pdb=" C SER B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.16 122.29 -4.13 7.00e-01 2.04e+00 3.49e+01 angle pdb=" CA SER D 85 " pdb=" C SER D 85 " pdb=" N PRO D 86 " ideal model delta sigma weight residual 118.16 122.28 -4.12 7.00e-01 2.04e+00 3.47e+01 angle pdb=" CA SER E 85 " pdb=" C SER E 85 " pdb=" N PRO E 86 " ideal model delta sigma weight residual 118.16 122.26 -4.10 7.00e-01 2.04e+00 3.44e+01 ... (remaining 6001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.54: 2223 10.54 - 21.07: 279 21.07 - 31.61: 48 31.61 - 42.14: 42 42.14 - 52.67: 12 Dihedral angle restraints: 2604 sinusoidal: 990 harmonic: 1614 Sorted by residual: dihedral pdb=" C TYR E 78 " pdb=" N TYR E 78 " pdb=" CA TYR E 78 " pdb=" CB TYR E 78 " ideal model delta harmonic sigma weight residual -122.60 -131.08 8.48 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" C TYR A 78 " pdb=" N TYR A 78 " pdb=" CA TYR A 78 " pdb=" CB TYR A 78 " ideal model delta harmonic sigma weight residual -122.60 -131.07 8.47 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" C TYR F 78 " pdb=" N TYR F 78 " pdb=" CA TYR F 78 " pdb=" CB TYR F 78 " ideal model delta harmonic sigma weight residual -122.60 -131.06 8.46 0 2.50e+00 1.60e-01 1.15e+01 ... (remaining 2601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 166 0.058 - 0.116: 256 0.116 - 0.174: 172 0.174 - 0.232: 65 0.232 - 0.290: 49 Chirality restraints: 708 Sorted by residual: chirality pdb=" CA ILE D 20 " pdb=" N ILE D 20 " pdb=" C ILE D 20 " pdb=" CB ILE D 20 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ILE B 20 " pdb=" N ILE B 20 " pdb=" C ILE B 20 " pdb=" CB ILE B 20 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ILE C 20 " pdb=" N ILE C 20 " pdb=" C ILE C 20 " pdb=" CB ILE C 20 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 705 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 118 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C THR C 118 " -0.040 2.00e-02 2.50e+03 pdb=" O THR C 118 " 0.015 2.00e-02 2.50e+03 pdb=" N THR C 119 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 118 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C THR E 118 " -0.040 2.00e-02 2.50e+03 pdb=" O THR E 118 " 0.015 2.00e-02 2.50e+03 pdb=" N THR E 119 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 118 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C THR A 118 " -0.040 2.00e-02 2.50e+03 pdb=" O THR A 118 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 119 " 0.014 2.00e-02 2.50e+03 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 10 2.37 - 3.00: 2431 3.00 - 3.63: 6016 3.63 - 4.27: 10325 4.27 - 4.90: 18821 Nonbonded interactions: 37603 Sorted by model distance: nonbonded pdb=" CB PHE D 64 " pdb=" CZ PHE E 64 " model vdw 1.732 3.740 nonbonded pdb=" CB PHE E 64 " pdb=" CZ PHE F 64 " model vdw 1.733 3.740 nonbonded pdb=" CB PHE C 64 " pdb=" CZ PHE D 64 " model vdw 1.733 3.740 nonbonded pdb=" CB PHE B 64 " pdb=" CZ PHE C 64 " model vdw 1.733 3.740 nonbonded pdb=" CB PHE A 64 " pdb=" CZ PHE B 64 " model vdw 1.733 3.740 ... (remaining 37598 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' } 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 individual isotropic 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.480 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.830 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.013 0.041 4416 Z= 0.863 Angle : 1.748 6.463 6006 Z= 1.298 Chirality : 0.128 0.290 708 Planarity : 0.005 0.023 738 Dihedral : 11.503 52.674 1560 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % 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: -3.31 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 79 HIS 0.005 0.001 HIS C 31 PHE 0.017 0.004 PHE A 87 TYR 0.010 0.002 TYR D 105 ARG 0.002 0.001 ARG F 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7787 (mtpp) REVERT: A 63 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7213 (mt-10) REVERT: A 76 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8365 (mttt) REVERT: B 23 SER cc_start: 0.9317 (m) cc_final: 0.8796 (t) REVERT: B 63 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7140 (mt-10) REVERT: B 115 SER cc_start: 0.8982 (t) cc_final: 0.8760 (t) REVERT: C 13 MET cc_start: 0.7403 (ttm) cc_final: 0.6275 (mpp) REVERT: C 15 LYS cc_start: 0.7697 (mtpt) cc_final: 0.7281 (mtpp) REVERT: C 23 SER cc_start: 0.9364 (m) cc_final: 0.8841 (t) REVERT: C 34 ARG cc_start: 0.6808 (ttt-90) cc_final: 0.6531 (ttt180) REVERT: C 63 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7425 (mt-10) REVERT: D 13 MET cc_start: 0.7412 (ttm) cc_final: 0.6538 (mpp) REVERT: D 23 SER cc_start: 0.9435 (m) cc_final: 0.9177 (m) REVERT: D 63 GLU cc_start: 0.7565 (mt-10) cc_final: 0.6791 (mt-10) REVERT: D 100 SER cc_start: 0.7727 (m) cc_final: 0.7495 (p) REVERT: E 13 MET cc_start: 0.7382 (ttm) cc_final: 0.6535 (mpp) REVERT: E 23 SER cc_start: 0.9418 (m) cc_final: 0.8883 (t) REVERT: E 34 ARG cc_start: 0.6757 (ttt-90) cc_final: 0.6437 (ttt90) REVERT: E 63 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6755 (mt-10) REVERT: F 13 MET cc_start: 0.7987 (ttm) cc_final: 0.7212 (mtm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2053 time to fit residues: 34.9933 Evaluate side-chains 121 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7628 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4416 Z= 0.243 Angle : 0.655 5.056 6006 Z= 0.373 Chirality : 0.053 0.160 708 Planarity : 0.005 0.035 738 Dihedral : 4.773 16.973 594 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.42 % Allowed : 12.39 % Favored : 84.19 % 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: -2.68 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.001 0.000 HIS F 90 PHE 0.035 0.003 PHE D 64 TYR 0.027 0.003 TYR B 114 ARG 0.002 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.448 Fit side-chains REVERT: A 35 LYS cc_start: 0.8004 (tttt) cc_final: 0.7779 (tmtt) REVERT: A 63 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7496 (tt0) REVERT: B 35 LYS cc_start: 0.8027 (tttp) cc_final: 0.7791 (tttt) REVERT: B 63 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7424 (mt-10) REVERT: C 13 MET cc_start: 0.7381 (ttm) cc_final: 0.6196 (mpp) REVERT: C 63 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7370 (tt0) REVERT: D 13 MET cc_start: 0.7330 (ttm) cc_final: 0.6406 (mpp) REVERT: D 23 SER cc_start: 0.9492 (m) cc_final: 0.8942 (m) REVERT: D 62 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7079 (mp0) REVERT: D 63 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7029 (tt0) REVERT: E 13 MET cc_start: 0.7388 (ttm) cc_final: 0.6468 (mpp) REVERT: E 23 SER cc_start: 0.9123 (m) cc_final: 0.8734 (t) REVERT: E 63 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6878 (tt0) REVERT: F 13 MET cc_start: 0.7973 (ttm) cc_final: 0.7168 (mtm) outliers start: 16 outliers final: 11 residues processed: 108 average time/residue: 0.1542 time to fit residues: 21.1486 Evaluate side-chains 110 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.7804 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4416 Z= 0.269 Angle : 0.580 4.231 6006 Z= 0.327 Chirality : 0.052 0.164 708 Planarity : 0.004 0.023 738 Dihedral : 5.128 18.197 594 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.42 % Allowed : 11.32 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 79 HIS 0.004 0.001 HIS A 31 PHE 0.017 0.003 PHE D 64 TYR 0.025 0.003 TYR B 114 ARG 0.003 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.474 Fit side-chains REVERT: A 63 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 116 TYR cc_start: 0.8766 (m-80) cc_final: 0.8512 (m-10) REVERT: B 117 SER cc_start: 0.9049 (p) cc_final: 0.8546 (m) REVERT: C 13 MET cc_start: 0.7410 (ttm) cc_final: 0.6203 (mpp) REVERT: D 13 MET cc_start: 0.7405 (ttm) cc_final: 0.6421 (mpp) REVERT: D 23 SER cc_start: 0.9403 (m) cc_final: 0.9198 (m) REVERT: E 13 MET cc_start: 0.7444 (ttm) cc_final: 0.6397 (mpp) REVERT: E 35 LYS cc_start: 0.8229 (tttt) cc_final: 0.8000 (mttt) REVERT: E 93 VAL cc_start: 0.9319 (t) cc_final: 0.9077 (p) REVERT: F 13 MET cc_start: 0.8091 (ttm) cc_final: 0.7121 (mtm) REVERT: F 35 LYS cc_start: 0.8649 (tttt) cc_final: 0.8377 (mttt) outliers start: 16 outliers final: 11 residues processed: 105 average time/residue: 0.1254 time to fit residues: 17.5737 Evaluate side-chains 108 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4416 Z= 0.382 Angle : 0.647 4.099 6006 Z= 0.369 Chirality : 0.053 0.152 708 Planarity : 0.004 0.027 738 Dihedral : 5.506 20.312 594 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.27 % Allowed : 11.97 % Favored : 83.76 % 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 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.005 0.001 HIS A 31 PHE 0.024 0.003 PHE F 64 TYR 0.024 0.003 TYR B 114 ARG 0.003 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.507 Fit side-chains REVERT: A 63 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7692 (mt-10) REVERT: B 117 SER cc_start: 0.9111 (p) cc_final: 0.8712 (m) REVERT: C 13 MET cc_start: 0.7492 (ttm) cc_final: 0.6175 (mpp) REVERT: D 13 MET cc_start: 0.7441 (ttm) cc_final: 0.6353 (mpp) REVERT: E 13 MET cc_start: 0.7529 (ttm) cc_final: 0.6399 (mpp) REVERT: E 92 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7426 (tm-30) REVERT: E 93 VAL cc_start: 0.9364 (t) cc_final: 0.9044 (p) REVERT: F 13 MET cc_start: 0.8233 (ttm) cc_final: 0.7170 (mpp) REVERT: F 63 GLU cc_start: 0.7838 (mt-10) cc_final: 0.6998 (tt0) outliers start: 20 outliers final: 13 residues processed: 111 average time/residue: 0.1223 time to fit residues: 18.1781 Evaluate side-chains 113 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4416 Z= 0.210 Angle : 0.541 3.935 6006 Z= 0.306 Chirality : 0.050 0.147 708 Planarity : 0.004 0.029 738 Dihedral : 5.252 18.859 594 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.35 % Allowed : 15.38 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 79 HIS 0.001 0.000 HIS B 90 PHE 0.020 0.002 PHE E 64 TYR 0.024 0.002 TYR E 114 ARG 0.001 0.000 ARG F 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.445 Fit side-chains REVERT: A 63 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 117 SER cc_start: 0.9010 (p) cc_final: 0.8715 (m) REVERT: B 76 LYS cc_start: 0.8370 (mttt) cc_final: 0.8104 (mtmm) REVERT: C 13 MET cc_start: 0.7500 (ttm) cc_final: 0.6200 (mpp) REVERT: D 13 MET cc_start: 0.7469 (ttm) cc_final: 0.6412 (mpp) REVERT: E 13 MET cc_start: 0.7511 (ttm) cc_final: 0.6366 (mpp) REVERT: E 23 SER cc_start: 0.9235 (m) cc_final: 0.8776 (t) REVERT: E 92 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7402 (tm-30) REVERT: E 93 VAL cc_start: 0.9337 (t) cc_final: 0.9055 (p) REVERT: F 13 MET cc_start: 0.8231 (ttm) cc_final: 0.7173 (mpp) outliers start: 11 outliers final: 8 residues processed: 101 average time/residue: 0.1234 time to fit residues: 16.6211 Evaluate side-chains 99 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 77 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4416 Z= 0.305 Angle : 0.591 4.134 6006 Z= 0.335 Chirality : 0.051 0.172 708 Planarity : 0.004 0.031 738 Dihedral : 5.318 19.039 594 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.78 % Allowed : 14.74 % Favored : 82.48 % 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: -2.39 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 79 HIS 0.003 0.001 HIS B 31 PHE 0.019 0.002 PHE E 64 TYR 0.025 0.002 TYR C 78 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.475 Fit side-chains REVERT: A 63 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7686 (mt-10) REVERT: B 117 SER cc_start: 0.9177 (p) cc_final: 0.8694 (m) REVERT: C 13 MET cc_start: 0.7443 (ttm) cc_final: 0.6246 (mpp) REVERT: D 13 MET cc_start: 0.7485 (ttm) cc_final: 0.6425 (mpp) REVERT: E 13 MET cc_start: 0.7552 (ttm) cc_final: 0.6390 (mpp) REVERT: E 23 SER cc_start: 0.9263 (m) cc_final: 0.8819 (t) REVERT: E 93 VAL cc_start: 0.9373 (t) cc_final: 0.9052 (p) REVERT: F 13 MET cc_start: 0.8279 (ttm) cc_final: 0.7231 (mpp) outliers start: 13 outliers final: 11 residues processed: 102 average time/residue: 0.1222 time to fit residues: 16.7772 Evaluate side-chains 101 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4416 Z= 0.200 Angle : 0.550 5.139 6006 Z= 0.309 Chirality : 0.050 0.147 708 Planarity : 0.004 0.031 738 Dihedral : 5.128 18.519 594 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.71 % Allowed : 15.81 % Favored : 82.48 % 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: -2.36 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 79 HIS 0.002 0.000 HIS E 90 PHE 0.026 0.002 PHE E 64 TYR 0.028 0.002 TYR C 78 ARG 0.001 0.000 ARG F 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.493 Fit side-chains REVERT: A 63 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7689 (mt-10) REVERT: B 76 LYS cc_start: 0.8331 (mttt) cc_final: 0.8099 (mtmm) REVERT: B 117 SER cc_start: 0.9107 (p) cc_final: 0.8578 (m) REVERT: C 13 MET cc_start: 0.7463 (ttm) cc_final: 0.6279 (mpp) REVERT: D 13 MET cc_start: 0.7429 (ttm) cc_final: 0.6364 (mpp) REVERT: E 13 MET cc_start: 0.7555 (ttm) cc_final: 0.6416 (mpp) REVERT: E 23 SER cc_start: 0.9232 (m) cc_final: 0.8753 (t) REVERT: F 13 MET cc_start: 0.8287 (ttm) cc_final: 0.7212 (mpt) outliers start: 8 outliers final: 7 residues processed: 97 average time/residue: 0.1254 time to fit residues: 16.3631 Evaluate side-chains 97 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 77 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4416 Z= 0.225 Angle : 0.554 5.343 6006 Z= 0.311 Chirality : 0.050 0.139 708 Planarity : 0.004 0.030 738 Dihedral : 5.090 17.934 594 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.50 % Allowed : 16.24 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 79 HIS 0.002 0.001 HIS B 31 PHE 0.023 0.002 PHE E 64 TYR 0.027 0.002 TYR E 114 ARG 0.001 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.525 Fit side-chains REVERT: A 63 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7726 (mt-10) REVERT: B 117 SER cc_start: 0.9090 (p) cc_final: 0.8615 (m) REVERT: C 13 MET cc_start: 0.7460 (ttm) cc_final: 0.6271 (mpp) REVERT: D 13 MET cc_start: 0.7444 (ttm) cc_final: 0.6347 (mpp) REVERT: E 13 MET cc_start: 0.7584 (ttm) cc_final: 0.6430 (mpp) REVERT: E 23 SER cc_start: 0.9242 (m) cc_final: 0.8767 (t) REVERT: F 13 MET cc_start: 0.8268 (ttm) cc_final: 0.7202 (mpt) REVERT: F 92 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7666 (tm-30) outliers start: 7 outliers final: 6 residues processed: 96 average time/residue: 0.1197 time to fit residues: 15.5884 Evaluate side-chains 97 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4416 Z= 0.274 Angle : 0.581 4.928 6006 Z= 0.327 Chirality : 0.051 0.157 708 Planarity : 0.004 0.030 738 Dihedral : 5.136 17.894 594 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.56 % Allowed : 15.17 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 79 HIS 0.002 0.001 HIS B 88 PHE 0.025 0.002 PHE E 64 TYR 0.031 0.003 TYR C 78 ARG 0.002 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.782 Fit side-chains REVERT: A 63 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7751 (mt-10) REVERT: B 117 SER cc_start: 0.9110 (p) cc_final: 0.8673 (m) REVERT: C 13 MET cc_start: 0.7460 (ttm) cc_final: 0.6263 (mpp) REVERT: C 110 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8494 (tp) REVERT: D 13 MET cc_start: 0.7464 (ttm) cc_final: 0.6364 (mpp) REVERT: E 13 MET cc_start: 0.7582 (ttm) cc_final: 0.6428 (mpp) REVERT: E 23 SER cc_start: 0.9245 (m) cc_final: 0.8771 (t) REVERT: E 92 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7488 (tm-30) REVERT: F 13 MET cc_start: 0.8292 (ttm) cc_final: 0.7227 (mpt) outliers start: 12 outliers final: 9 residues processed: 98 average time/residue: 0.1132 time to fit residues: 15.5122 Evaluate side-chains 100 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.0370 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4416 Z= 0.200 Angle : 0.551 6.328 6006 Z= 0.308 Chirality : 0.050 0.141 708 Planarity : 0.004 0.031 738 Dihedral : 5.003 18.533 594 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.28 % Allowed : 16.67 % Favored : 82.05 % 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: -2.37 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 79 HIS 0.001 0.000 HIS A 31 PHE 0.024 0.002 PHE E 64 TYR 0.032 0.002 TYR C 78 ARG 0.002 0.000 ARG D 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.478 Fit side-chains REVERT: A 63 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7731 (mt-10) REVERT: B 117 SER cc_start: 0.9018 (p) cc_final: 0.8628 (m) REVERT: C 13 MET cc_start: 0.7455 (ttm) cc_final: 0.6249 (mpp) REVERT: C 34 ARG cc_start: 0.6853 (ttt-90) cc_final: 0.6547 (tpp80) REVERT: C 110 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8339 (tp) REVERT: D 13 MET cc_start: 0.7459 (ttm) cc_final: 0.6352 (mpp) REVERT: E 13 MET cc_start: 0.7562 (ttm) cc_final: 0.6389 (mpp) REVERT: E 23 SER cc_start: 0.9244 (m) cc_final: 0.8764 (t) REVERT: F 13 MET cc_start: 0.8268 (ttm) cc_final: 0.7219 (mpt) REVERT: F 80 LYS cc_start: 0.7988 (tttt) cc_final: 0.7749 (tttm) outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 0.1483 time to fit residues: 18.6223 Evaluate side-chains 95 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain F residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.146705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.114716 restraints weight = 5154.154| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.56 r_work: 0.3970 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4416 Z= 0.351 Angle : 0.631 5.525 6006 Z= 0.358 Chirality : 0.052 0.158 708 Planarity : 0.004 0.029 738 Dihedral : 5.272 18.536 594 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.28 % Allowed : 15.81 % Favored : 82.91 % 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: -2.50 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.004 0.001 HIS B 88 PHE 0.018 0.002 PHE E 64 TYR 0.040 0.003 TYR D 78 ARG 0.003 0.001 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.08 seconds wall clock time: 27 minutes 5.88 seconds (1625.88 seconds total)