Starting phenix.real_space_refine on Mon Mar 11 07:32:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/03_2024/8ehs_28151.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/03_2024/8ehs_28151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/03_2024/8ehs_28151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/03_2024/8ehs_28151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/03_2024/8ehs_28151.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/03_2024/8ehs_28151.pdb" } resolution = 3.3 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= 0.014 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 21 5.16 5 C 4676 2.51 5 N 1253 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 129": "OE1" <-> "OE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ASP 93": "OD1" <-> "OD2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F ASP 93": "OD1" <-> "OD2" Residue "F GLU 95": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7546 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "A" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "B" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "C" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "D" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "E" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "F" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Time building chain proxies: 4.58, per 1000 atoms: 0.61 Number of scatterers: 7546 At special positions: 0 Unit cell: (85.162, 85.162, 99.176, 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 21 16.00 O 1596 8.00 N 1253 7.00 C 4676 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: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 26 sheets defined 3.6% alpha, 54.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.622A pdb=" N ASN D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'F' and resid 97 through 102 removed outlier: 3.654A pdb=" N ASN F 102 " --> pdb=" O VAL F 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 8.254A pdb=" N ILE A 29 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR G 6 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU A 31 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG G 8 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N TYR A 33 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER G 10 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE A 136 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 67 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 8.254A pdb=" N ILE A 29 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR G 6 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU A 31 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG G 8 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N TYR A 33 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER G 10 " --> pdb=" O TYR A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 15 through 19 removed outlier: 4.385A pdb=" N ILE G 49 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER G 113 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR G 51 " --> pdb=" O VAL G 111 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL G 111 " --> pdb=" O THR G 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 33 through 34 removed outlier: 3.507A pdb=" N SER G 34 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN G 39 " --> pdb=" O SER G 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 94 through 96 removed outlier: 3.621A pdb=" N GLY G 57 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.165A pdb=" N ILE B 29 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A 6 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE B 136 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL B 67 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.165A pdb=" N ILE B 29 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A 6 " --> pdb=" O ILE B 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 15 through 19 removed outlier: 4.587A pdb=" N ILE A 49 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER A 113 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR A 51 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL A 111 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 15 through 19 removed outlier: 4.621A pdb=" N ILE C 49 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N SER C 113 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR C 51 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL C 111 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL C 67 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE C 136 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.083A pdb=" N ILE C 29 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR B 6 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU C 31 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG B 8 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE C 136 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL C 67 " --> pdb=" O ILE C 136 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 77 through 84 current: chain 'C' and resid 94 through 96 Processing sheet with id=AB3, first strand: chain 'B' and resid 15 through 19 Processing sheet with id=AB4, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.575A pdb=" N ASN B 39 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 28 through 31 removed outlier: 8.466A pdb=" N ILE D 29 " --> pdb=" O ASN C 4 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 6 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU D 31 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG C 8 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE D 136 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL D 67 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 28 through 31 removed outlier: 8.466A pdb=" N ILE D 29 " --> pdb=" O ASN C 4 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 6 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU D 31 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG C 8 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.591A pdb=" N ASN C 39 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 28 through 31 removed outlier: 8.424A pdb=" N ILE E 29 " --> pdb=" O ASN D 4 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR D 6 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU E 31 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG D 8 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE E 136 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL E 67 " --> pdb=" O ILE E 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 28 through 31 removed outlier: 8.424A pdb=" N ILE E 29 " --> pdb=" O ASN D 4 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR D 6 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU E 31 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG D 8 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 15 through 19 removed outlier: 4.482A pdb=" N ILE D 49 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER D 113 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR D 51 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL D 111 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 33 through 34 removed outlier: 3.501A pdb=" N SER D 34 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 39 " --> pdb=" O SER D 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 28 through 30 removed outlier: 8.400A pdb=" N ILE F 29 " --> pdb=" O ASN E 4 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR E 6 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 131 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE F 136 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL F 67 " --> pdb=" O ILE F 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 28 through 30 removed outlier: 8.400A pdb=" N ILE F 29 " --> pdb=" O ASN E 4 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR E 6 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 131 " --> pdb=" O VAL E 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 15 through 19 removed outlier: 4.239A pdb=" N ILE E 49 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER E 113 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR E 51 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL E 111 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 33 through 34 removed outlier: 3.580A pdb=" N ASN E 39 " --> pdb=" O SER E 34 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 15 through 19 removed outlier: 4.370A pdb=" N ILE F 49 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N SER F 113 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR F 51 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL F 111 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 33 through 34 removed outlier: 3.533A pdb=" N SER F 34 " --> pdb=" O ASN F 39 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN F 39 " --> pdb=" O SER F 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 306 hydrogen bonds defined for protein. 762 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: 2.12 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2506 1.34 - 1.46: 1474 1.46 - 1.58: 3615 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 7637 Sorted by residual: bond pdb=" N VAL G 1 " pdb=" CA VAL G 1 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.39e+00 bond pdb=" N VAL E 1 " pdb=" CA VAL E 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N VAL C 1 " pdb=" CA VAL C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N VAL B 1 " pdb=" CA VAL B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N VAL F 1 " pdb=" CA VAL F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 7632 not shown) Histogram of bond angle deviations from ideal: 100.69 - 106.82: 204 106.82 - 112.94: 4494 112.94 - 119.06: 1903 119.06 - 125.18: 3752 125.18 - 131.31: 56 Bond angle restraints: 10409 Sorted by residual: angle pdb=" C ASP A 93 " pdb=" CA ASP A 93 " pdb=" CB ASP A 93 " ideal model delta sigma weight residual 109.54 112.42 -2.88 1.84e+00 2.95e-01 2.45e+00 angle pdb=" N MET E 72 " pdb=" CA MET E 72 " pdb=" C MET E 72 " ideal model delta sigma weight residual 111.36 113.00 -1.64 1.09e+00 8.42e-01 2.27e+00 angle pdb=" N MET D 72 " pdb=" CA MET D 72 " pdb=" C MET D 72 " ideal model delta sigma weight residual 111.36 112.98 -1.62 1.09e+00 8.42e-01 2.20e+00 angle pdb=" N MET G 72 " pdb=" CA MET G 72 " pdb=" C MET G 72 " ideal model delta sigma weight residual 111.36 112.97 -1.61 1.09e+00 8.42e-01 2.18e+00 angle pdb=" CA GLN A 124 " pdb=" C GLN A 124 " pdb=" N GLY A 125 " ideal model delta sigma weight residual 114.90 116.86 -1.96 1.37e+00 5.33e-01 2.04e+00 ... (remaining 10404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4342 17.95 - 35.90: 264 35.90 - 53.85: 42 53.85 - 71.80: 19 71.80 - 89.75: 16 Dihedral angle restraints: 4683 sinusoidal: 1750 harmonic: 2933 Sorted by residual: dihedral pdb=" CA ASP C 99 " pdb=" CB ASP C 99 " pdb=" CG ASP C 99 " pdb=" OD1 ASP C 99 " ideal model delta sinusoidal sigma weight residual -30.00 -91.71 61.71 1 2.00e+01 2.50e-03 1.26e+01 dihedral pdb=" CB GLU E 95 " pdb=" CG GLU E 95 " pdb=" CD GLU E 95 " pdb=" OE1 GLU E 95 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 129 " pdb=" CG GLU D 129 " pdb=" CD GLU D 129 " pdb=" OE1 GLU D 129 " ideal model delta sinusoidal sigma weight residual 0.00 89.38 -89.38 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 758 0.029 - 0.057: 386 0.057 - 0.086: 38 0.086 - 0.114: 111 0.114 - 0.143: 30 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA VAL D 1 " pdb=" N VAL D 1 " pdb=" C VAL D 1 " pdb=" CB VAL D 1 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA VAL B 1 " pdb=" N VAL B 1 " pdb=" C VAL B 1 " pdb=" CB VAL B 1 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA VAL E 1 " pdb=" N VAL E 1 " pdb=" C VAL E 1 " pdb=" CB VAL E 1 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 1320 not shown) Planarity restraints: 1337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 142 " 0.023 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C THR E 142 " -0.080 2.00e-02 2.50e+03 pdb=" O THR E 142 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN E 143 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 142 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C THR B 142 " -0.080 2.00e-02 2.50e+03 pdb=" O THR B 142 " 0.030 2.00e-02 2.50e+03 pdb=" N GLN B 143 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 142 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C THR C 142 " 0.079 2.00e-02 2.50e+03 pdb=" O THR C 142 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN C 143 " -0.026 2.00e-02 2.50e+03 ... (remaining 1334 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 101 2.65 - 3.21: 6867 3.21 - 3.77: 10358 3.77 - 4.34: 15566 4.34 - 4.90: 26430 Nonbonded interactions: 59322 Sorted by model distance: nonbonded pdb=" OG SER G 63 " pdb=" OG SER G 138 " model vdw 2.082 2.440 nonbonded pdb=" OG SER D 63 " pdb=" OG SER D 138 " model vdw 2.090 2.440 nonbonded pdb=" OG SER F 63 " pdb=" OG SER F 138 " model vdw 2.117 2.440 nonbonded pdb=" OG SER E 63 " pdb=" OG SER E 138 " model vdw 2.122 2.440 nonbonded pdb=" OG SER B 63 " pdb=" OG SER B 138 " model vdw 2.146 2.440 ... (remaining 59317 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' } 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=0.00 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: 0.320 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: 2.190 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.310 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.002 0.035 7637 Z= 0.156 Angle : 0.471 3.830 10409 Z= 0.263 Chirality : 0.044 0.143 1323 Planarity : 0.004 0.047 1337 Dihedral : 14.122 89.752 2779 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 1001 helix: None (None), residues: 0 sheet: 0.86 (0.24), residues: 406 loop : 1.29 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 120 PHE 0.004 0.001 PHE E 96 TYR 0.004 0.001 TYR C 133 ARG 0.001 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.906 Fit side-chains REVERT: G 14 LYS cc_start: 0.7176 (mttm) cc_final: 0.6912 (mtpt) REVERT: A 87 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8190 (ptpt) REVERT: A 137 ILE cc_start: 0.8445 (mm) cc_final: 0.8228 (mt) REVERT: C 39 ASN cc_start: 0.8608 (t0) cc_final: 0.8216 (t0) REVERT: C 126 THR cc_start: 0.7962 (m) cc_final: 0.7426 (p) REVERT: C 141 MET cc_start: 0.8911 (ttp) cc_final: 0.8470 (mtm) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1928 time to fit residues: 30.7238 Evaluate side-chains 92 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0870 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN B 115 GLN B 143 GLN D 38 ASN E 38 ASN F 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7637 Z= 0.169 Angle : 0.503 4.494 10409 Z= 0.271 Chirality : 0.046 0.161 1323 Planarity : 0.003 0.027 1337 Dihedral : 6.810 72.675 1043 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.67 % Allowed : 4.27 % Favored : 95.05 % 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: 0.94 (0.26), residues: 1001 helix: -3.25 (0.58), residues: 42 sheet: 1.27 (0.28), residues: 322 loop : 0.68 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.008 0.001 PHE D 96 TYR 0.006 0.001 TYR A 133 ARG 0.003 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.811 Fit side-chains REVERT: G 69 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8600 (t) REVERT: C 126 THR cc_start: 0.7900 (m) cc_final: 0.7488 (p) REVERT: C 141 MET cc_start: 0.8937 (ttp) cc_final: 0.8505 (mtm) REVERT: D 47 THR cc_start: 0.8806 (p) cc_final: 0.8606 (p) REVERT: D 72 MET cc_start: 0.7470 (mmm) cc_final: 0.7176 (mmm) outliers start: 6 outliers final: 5 residues processed: 111 average time/residue: 0.1822 time to fit residues: 28.0813 Evaluate side-chains 95 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain D residue 16 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN A 110 ASN A 116 GLN C 38 ASN D 4 ASN D 115 GLN E 38 ASN E 115 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 7637 Z= 0.511 Angle : 0.705 7.395 10409 Z= 0.371 Chirality : 0.054 0.171 1323 Planarity : 0.004 0.038 1337 Dihedral : 7.358 75.678 1043 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.59 % Allowed : 9.56 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1001 helix: -3.63 (0.46), residues: 42 sheet: 1.04 (0.26), residues: 336 loop : 0.25 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 120 PHE 0.014 0.002 PHE D 40 TYR 0.009 0.003 TYR F 133 ARG 0.003 0.001 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.905 Fit side-chains REVERT: A 116 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7949 (mm-40) REVERT: C 126 THR cc_start: 0.8349 (m) cc_final: 0.7958 (p) REVERT: E 69 SER cc_start: 0.8637 (t) cc_final: 0.8295 (p) REVERT: F 24 SER cc_start: 0.8631 (p) cc_final: 0.8182 (t) outliers start: 23 outliers final: 21 residues processed: 116 average time/residue: 0.1818 time to fit residues: 29.7534 Evaluate side-chains 105 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain F residue 106 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 0.0470 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 116 GLN A 116 GLN E 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7637 Z= 0.183 Angle : 0.477 4.137 10409 Z= 0.256 Chirality : 0.045 0.146 1323 Planarity : 0.003 0.030 1337 Dihedral : 6.449 75.352 1043 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.04 % Allowed : 12.94 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1001 helix: -3.38 (0.53), residues: 42 sheet: 1.14 (0.27), residues: 329 loop : 0.37 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.006 0.001 PHE E 96 TYR 0.004 0.001 TYR B 133 ARG 0.002 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 0.897 Fit side-chains REVERT: G 6 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8481 (m) REVERT: G 14 LYS cc_start: 0.7391 (mttm) cc_final: 0.6874 (mtpt) REVERT: G 69 SER cc_start: 0.8830 (p) cc_final: 0.8531 (t) REVERT: A 72 MET cc_start: 0.6807 (mmm) cc_final: 0.6599 (mmm) REVERT: A 118 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.7793 (m) REVERT: C 126 THR cc_start: 0.8156 (m) cc_final: 0.7704 (p) REVERT: D 105 THR cc_start: 0.8238 (p) cc_final: 0.8000 (p) REVERT: E 6 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8507 (m) REVERT: E 69 SER cc_start: 0.8630 (t) cc_final: 0.8311 (p) REVERT: F 87 LYS cc_start: 0.8009 (ptpp) cc_final: 0.7539 (ptpt) outliers start: 27 outliers final: 20 residues processed: 105 average time/residue: 0.1578 time to fit residues: 23.8710 Evaluate side-chains 108 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 106 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN A 143 GLN D 143 GLN F 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 7637 Z= 0.453 Angle : 0.652 6.525 10409 Z= 0.345 Chirality : 0.051 0.164 1323 Planarity : 0.004 0.042 1337 Dihedral : 7.081 83.377 1043 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.85 % Allowed : 11.81 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1001 helix: -3.47 (0.51), residues: 42 sheet: 0.80 (0.26), residues: 336 loop : 0.02 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 120 PHE 0.012 0.002 PHE D 40 TYR 0.009 0.002 TYR E 133 ARG 0.003 0.001 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 86 time to evaluate : 0.895 Fit side-chains REVERT: A 72 MET cc_start: 0.7164 (mmm) cc_final: 0.6807 (mmm) REVERT: A 118 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.7929 (m) REVERT: C 126 THR cc_start: 0.8405 (m) cc_final: 0.8006 (p) REVERT: E 69 SER cc_start: 0.8593 (t) cc_final: 0.8287 (p) REVERT: F 24 SER cc_start: 0.8641 (p) cc_final: 0.8184 (t) REVERT: F 87 LYS cc_start: 0.8014 (ptpp) cc_final: 0.7528 (ptpt) outliers start: 52 outliers final: 44 residues processed: 124 average time/residue: 0.1498 time to fit residues: 27.1940 Evaluate side-chains 128 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 83 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7637 Z= 0.121 Angle : 0.433 3.353 10409 Z= 0.233 Chirality : 0.043 0.136 1323 Planarity : 0.003 0.028 1337 Dihedral : 6.018 83.130 1043 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.92 % Allowed : 15.19 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1001 helix: -3.17 (0.58), residues: 42 sheet: 0.69 (0.26), residues: 364 loop : 0.57 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.006 0.001 PHE E 96 TYR 0.003 0.000 TYR E 33 ARG 0.001 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.869 Fit side-chains REVERT: G 6 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8513 (m) REVERT: G 14 LYS cc_start: 0.7304 (mttm) cc_final: 0.6857 (mtpt) REVERT: G 69 SER cc_start: 0.8824 (p) cc_final: 0.8494 (t) REVERT: A 72 MET cc_start: 0.6860 (mmm) cc_final: 0.6547 (mmm) REVERT: A 118 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.7907 (m) REVERT: C 126 THR cc_start: 0.8044 (m) cc_final: 0.7599 (p) REVERT: C 141 MET cc_start: 0.8889 (ttp) cc_final: 0.8502 (mtm) REVERT: D 105 THR cc_start: 0.8077 (p) cc_final: 0.7862 (p) REVERT: E 69 SER cc_start: 0.8604 (t) cc_final: 0.8387 (p) REVERT: F 87 LYS cc_start: 0.7961 (ptpp) cc_final: 0.7472 (ptpt) outliers start: 26 outliers final: 21 residues processed: 106 average time/residue: 0.1530 time to fit residues: 23.9118 Evaluate side-chains 108 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7637 Z= 0.265 Angle : 0.516 4.880 10409 Z= 0.273 Chirality : 0.046 0.149 1323 Planarity : 0.003 0.030 1337 Dihedral : 6.315 87.037 1043 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.94 % Allowed : 15.52 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1001 helix: -3.19 (0.57), residues: 42 sheet: 0.93 (0.27), residues: 329 loop : 0.32 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.007 0.001 PHE D 40 TYR 0.006 0.001 TYR F 133 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 86 time to evaluate : 0.929 Fit side-chains REVERT: G 14 LYS cc_start: 0.7395 (mttm) cc_final: 0.6936 (mtpt) REVERT: A 72 MET cc_start: 0.7101 (mmm) cc_final: 0.6758 (mmm) REVERT: A 118 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7870 (m) REVERT: A 122 ASP cc_start: 0.7639 (p0) cc_final: 0.7360 (p0) REVERT: C 126 THR cc_start: 0.8318 (m) cc_final: 0.7940 (p) REVERT: D 105 THR cc_start: 0.8140 (p) cc_final: 0.7931 (p) REVERT: E 69 SER cc_start: 0.8658 (t) cc_final: 0.8361 (p) REVERT: F 87 LYS cc_start: 0.8033 (ptpp) cc_final: 0.7535 (ptpt) outliers start: 35 outliers final: 30 residues processed: 110 average time/residue: 0.1405 time to fit residues: 23.0717 Evaluate side-chains 117 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 86 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 7637 Z= 0.455 Angle : 0.647 6.497 10409 Z= 0.342 Chirality : 0.051 0.160 1323 Planarity : 0.004 0.037 1337 Dihedral : 7.014 85.951 1043 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.84 % Allowed : 14.74 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1001 helix: -3.29 (0.54), residues: 42 sheet: 0.56 (0.27), residues: 329 loop : -0.02 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 120 PHE 0.011 0.002 PHE D 40 TYR 0.009 0.002 TYR E 133 ARG 0.003 0.001 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 83 time to evaluate : 0.834 Fit side-chains REVERT: A 72 MET cc_start: 0.7351 (mmm) cc_final: 0.6868 (mmm) REVERT: A 118 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.7952 (m) REVERT: C 126 THR cc_start: 0.8458 (m) cc_final: 0.8024 (p) REVERT: E 69 SER cc_start: 0.8558 (t) cc_final: 0.8231 (p) REVERT: F 87 LYS cc_start: 0.8004 (ptpp) cc_final: 0.7516 (ptpt) outliers start: 43 outliers final: 35 residues processed: 113 average time/residue: 0.1549 time to fit residues: 25.6359 Evaluate side-chains 117 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 81 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.7830 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7637 Z= 0.213 Angle : 0.493 4.636 10409 Z= 0.263 Chirality : 0.045 0.144 1323 Planarity : 0.003 0.034 1337 Dihedral : 6.332 82.096 1043 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.60 % Allowed : 16.31 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1001 helix: -3.19 (0.57), residues: 42 sheet: 0.29 (0.26), residues: 364 loop : 0.34 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.007 0.001 PHE E 96 TYR 0.004 0.001 TYR F 133 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 91 time to evaluate : 0.880 Fit side-chains REVERT: G 6 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8491 (m) REVERT: G 14 LYS cc_start: 0.7319 (mttm) cc_final: 0.6867 (mtpt) REVERT: A 72 MET cc_start: 0.7263 (mmm) cc_final: 0.6743 (mmm) REVERT: A 118 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7873 (m) REVERT: A 137 ILE cc_start: 0.8738 (mm) cc_final: 0.8409 (mm) REVERT: C 126 THR cc_start: 0.8396 (m) cc_final: 0.7987 (p) REVERT: D 105 THR cc_start: 0.8210 (p) cc_final: 0.7986 (p) REVERT: E 32 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8536 (p) REVERT: E 69 SER cc_start: 0.8599 (t) cc_final: 0.8265 (p) REVERT: F 87 LYS cc_start: 0.8032 (ptpp) cc_final: 0.7540 (ptpt) outliers start: 32 outliers final: 28 residues processed: 110 average time/residue: 0.1555 time to fit residues: 24.9500 Evaluate side-chains 121 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7637 Z= 0.280 Angle : 0.535 6.306 10409 Z= 0.284 Chirality : 0.047 0.150 1323 Planarity : 0.004 0.035 1337 Dihedral : 6.209 76.080 1043 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.39 % Allowed : 15.41 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1001 helix: -3.20 (0.56), residues: 42 sheet: 0.59 (0.27), residues: 329 loop : 0.16 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 120 PHE 0.007 0.001 PHE D 40 TYR 0.006 0.001 TYR G 133 ARG 0.001 0.000 ARG A 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 86 time to evaluate : 0.849 Fit side-chains REVERT: G 14 LYS cc_start: 0.7391 (mttm) cc_final: 0.6926 (mtpt) REVERT: A 72 MET cc_start: 0.7310 (mmm) cc_final: 0.6787 (mmm) REVERT: A 118 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.7908 (m) REVERT: C 126 THR cc_start: 0.8463 (m) cc_final: 0.8060 (p) REVERT: D 105 THR cc_start: 0.8224 (p) cc_final: 0.7999 (p) REVERT: E 32 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8549 (p) REVERT: E 69 SER cc_start: 0.8615 (t) cc_final: 0.8259 (p) REVERT: F 87 LYS cc_start: 0.8053 (ptpp) cc_final: 0.7546 (ptpt) outliers start: 39 outliers final: 36 residues processed: 111 average time/residue: 0.1509 time to fit residues: 24.6666 Evaluate side-chains 124 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 86 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 68 optimal weight: 0.1980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.114678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.107436 restraints weight = 8667.026| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 0.84 r_work: 0.3008 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7637 Z= 0.203 Angle : 0.483 5.247 10409 Z= 0.257 Chirality : 0.045 0.143 1323 Planarity : 0.003 0.034 1337 Dihedral : 5.736 69.876 1043 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.94 % Allowed : 15.97 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1001 helix: -3.15 (0.57), residues: 42 sheet: 0.35 (0.26), residues: 364 loop : 0.45 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.006 0.001 PHE E 96 TYR 0.004 0.001 TYR F 133 ARG 0.001 0.000 ARG A 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.87 seconds wall clock time: 30 minutes 21.88 seconds (1821.88 seconds total)