Starting phenix.real_space_refine on Tue Sep 24 07:33:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/09_2024/8ehs_28151.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/09_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_28151/09_2024/8ehs_28151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/09_2024/8ehs_28151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/09_2024/8ehs_28151.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/09_2024/8ehs_28151.cif" } 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. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.18, per 1000 atoms: 0.69 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 - 3.00 Amino acid : True - 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: 1.95 Conformation dependent library (CDL) restraints added in 1.2 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: 1.35 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: 2.09 Time building geometry restraints manager: 2.26 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: 0.00 - 0.77: 9658 0.77 - 1.53: 623 1.53 - 2.30: 73 2.30 - 3.06: 14 3.06 - 3.83: 41 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 3.040 nonbonded pdb=" OG SER D 63 " pdb=" OG SER D 138 " model vdw 2.090 3.040 nonbonded pdb=" OG SER F 63 " pdb=" OG SER F 138 " model vdw 2.117 3.040 nonbonded pdb=" OG SER E 63 " pdb=" OG SER E 138 " model vdw 2.122 3.040 nonbonded pdb=" OG SER B 63 " pdb=" OG SER B 138 " model vdw 2.146 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.580 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- 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 : 0.841 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: 0.1974 time to fit residues: 31.6583 Evaluate side-chains 92 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 0.5980 chunk 74 optimal weight: 6.9990 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: 6.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN D 38 ASN D 115 GLN E 38 ASN E 115 GLN F 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7637 Z= 0.257 Angle : 0.571 4.895 10409 Z= 0.306 Chirality : 0.048 0.169 1323 Planarity : 0.003 0.026 1337 Dihedral : 7.118 73.423 1043 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.24 % Allowed : 4.61 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1001 helix: -3.51 (0.51), residues: 42 sheet: 1.16 (0.28), residues: 322 loop : 0.62 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.010 0.001 PHE D 40 TYR 0.008 0.001 TYR A 133 ARG 0.002 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 122 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.893 Fit side-chains REVERT: G 39 ASN cc_start: 0.8783 (t0) cc_final: 0.8557 (t0) REVERT: G 69 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8598 (t) REVERT: G 141 MET cc_start: 0.8421 (mtm) cc_final: 0.8040 (mtp) REVERT: C 52 ASN cc_start: 0.7424 (t0) cc_final: 0.7120 (t0) REVERT: C 126 THR cc_start: 0.8192 (m) cc_final: 0.7758 (p) REVERT: C 141 MET cc_start: 0.8902 (ttp) cc_final: 0.8470 (mtm) REVERT: D 72 MET cc_start: 0.7471 (mmm) cc_final: 0.7250 (mmm) REVERT: D 105 THR cc_start: 0.8197 (p) cc_final: 0.7948 (p) outliers start: 11 outliers final: 9 residues processed: 118 average time/residue: 0.1876 time to fit residues: 30.4341 Evaluate side-chains 97 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 51 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR 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 F residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 D 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7637 Z= 0.254 Angle : 0.536 4.940 10409 Z= 0.287 Chirality : 0.047 0.155 1323 Planarity : 0.003 0.029 1337 Dihedral : 6.519 69.916 1043 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.91 % Allowed : 10.46 % Favored : 87.63 % 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: 0.56 (0.25), residues: 1001 helix: -3.71 (0.44), residues: 42 sheet: 0.92 (0.26), residues: 350 loop : 0.47 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.009 0.001 PHE D 40 TYR 0.005 0.001 TYR F 133 ARG 0.003 0.001 ARG D 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 112 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.902 Fit side-chains REVERT: C 126 THR cc_start: 0.8210 (m) cc_final: 0.7781 (p) REVERT: D 105 THR cc_start: 0.8234 (p) cc_final: 0.8015 (p) REVERT: E 6 THR cc_start: 0.8961 (t) cc_final: 0.8501 (m) REVERT: E 69 SER cc_start: 0.8657 (t) cc_final: 0.8343 (p) REVERT: F 87 LYS cc_start: 0.8050 (ptpp) cc_final: 0.7555 (ptpt) REVERT: F 129 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6669 (mp0) outliers start: 17 outliers final: 14 residues processed: 105 average time/residue: 0.1715 time to fit residues: 25.5594 Evaluate side-chains 102 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 141 MET 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 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 100 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: 1.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 78 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 F 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7637 Z= 0.265 Angle : 0.535 5.117 10409 Z= 0.287 Chirality : 0.047 0.153 1323 Planarity : 0.003 0.031 1337 Dihedral : 6.103 67.213 1043 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.49 % Allowed : 11.81 % Favored : 84.70 % 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: 0.56 (0.25), residues: 1001 helix: -3.56 (0.48), residues: 42 sheet: 1.03 (0.27), residues: 329 loop : 0.40 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.008 0.001 PHE D 40 TYR 0.005 0.001 TYR G 133 ARG 0.002 0.000 ARG A 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 124 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 0.909 Fit side-chains REVERT: A 72 MET cc_start: 0.7008 (mmm) cc_final: 0.6650 (mmm) REVERT: A 118 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.7857 (m) REVERT: C 126 THR cc_start: 0.8229 (m) cc_final: 0.7870 (p) REVERT: D 105 THR cc_start: 0.8188 (p) cc_final: 0.7960 (p) REVERT: E 69 SER cc_start: 0.8672 (t) cc_final: 0.8372 (p) REVERT: F 87 LYS cc_start: 0.8047 (ptpp) cc_final: 0.7568 (ptpt) REVERT: F 129 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6720 (mp0) outliers start: 31 outliers final: 24 residues processed: 114 average time/residue: 0.1667 time to fit residues: 27.0927 Evaluate side-chains 113 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 112 SER 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 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 51 THR 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 91 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 32 THR Chi-restraints excluded: chain E residue 100 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7637 Z= 0.240 Angle : 0.514 5.152 10409 Z= 0.275 Chirality : 0.046 0.150 1323 Planarity : 0.003 0.029 1337 Dihedral : 5.811 62.661 1043 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.26 % Allowed : 13.72 % Favored : 83.01 % 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 (0.25), residues: 1001 helix: -3.53 (0.49), residues: 42 sheet: 0.94 (0.27), residues: 329 loop : 0.34 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.007 0.001 PHE D 40 TYR 0.005 0.001 TYR G 133 ARG 0.002 0.000 ARG D 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 117 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 0.841 Fit side-chains REVERT: G 6 THR cc_start: 0.8873 (t) cc_final: 0.8509 (m) REVERT: G 14 LYS cc_start: 0.7340 (mttm) cc_final: 0.6832 (mtpt) REVERT: G 138 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.8010 (m) REVERT: A 72 MET cc_start: 0.7102 (mmm) cc_final: 0.6675 (mmm) REVERT: A 118 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.7847 (m) REVERT: C 126 THR cc_start: 0.8248 (m) cc_final: 0.7820 (p) REVERT: D 105 THR cc_start: 0.8159 (p) cc_final: 0.7948 (p) REVERT: E 69 SER cc_start: 0.8656 (t) cc_final: 0.8357 (p) REVERT: F 87 LYS cc_start: 0.8036 (ptpp) cc_final: 0.7549 (ptpt) REVERT: F 129 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6684 (mp0) outliers start: 29 outliers final: 25 residues processed: 107 average time/residue: 0.1694 time to fit residues: 25.9081 Evaluate side-chains 111 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 138 SER 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 44 SER 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 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 91 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 32 THR Chi-restraints excluded: chain E residue 97 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7637 Z= 0.286 Angle : 0.546 5.482 10409 Z= 0.290 Chirality : 0.047 0.152 1323 Planarity : 0.003 0.030 1337 Dihedral : 5.800 54.020 1043 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.27 % Allowed : 13.84 % 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: 0.31 (0.25), residues: 1001 helix: -3.52 (0.49), residues: 42 sheet: 0.82 (0.27), residues: 329 loop : 0.23 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.007 0.001 PHE D 40 TYR 0.006 0.001 TYR E 133 ARG 0.002 0.000 ARG A 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 130 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 0.907 Fit side-chains REVERT: G 14 LYS cc_start: 0.7390 (mttm) cc_final: 0.6881 (mtpt) REVERT: A 118 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.7887 (m) REVERT: C 126 THR cc_start: 0.8282 (m) cc_final: 0.7934 (p) REVERT: D 105 THR cc_start: 0.8179 (p) cc_final: 0.7970 (p) REVERT: E 69 SER cc_start: 0.8600 (t) cc_final: 0.8352 (p) REVERT: E 122 ASP cc_start: 0.8475 (t0) cc_final: 0.8241 (t0) REVERT: F 87 LYS cc_start: 0.8049 (ptpp) cc_final: 0.7564 (ptpt) outliers start: 38 outliers final: 32 residues processed: 117 average time/residue: 0.1603 time to fit residues: 27.0606 Evaluate side-chains 123 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 90 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 138 SER 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 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 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 100 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 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 E residue 100 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7793 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7637 Z= 0.155 Angle : 0.462 4.238 10409 Z= 0.248 Chirality : 0.044 0.143 1323 Planarity : 0.003 0.026 1337 Dihedral : 5.135 40.997 1043 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.26 % Allowed : 15.52 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1001 helix: -3.48 (0.49), residues: 42 sheet: 0.56 (0.26), residues: 364 loop : 0.55 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.006 0.001 PHE E 96 TYR 0.004 0.001 TYR G 133 ARG 0.002 0.000 ARG D 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 116 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 87 time to evaluate : 0.885 Fit side-chains REVERT: G 6 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8509 (m) REVERT: G 14 LYS cc_start: 0.7329 (mttm) cc_final: 0.6894 (mtpt) REVERT: G 138 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.8067 (m) REVERT: A 72 MET cc_start: 0.7028 (mmm) cc_final: 0.6628 (mmm) REVERT: C 126 THR cc_start: 0.8190 (m) cc_final: 0.7759 (p) REVERT: E 69 SER cc_start: 0.8633 (t) cc_final: 0.8395 (p) outliers start: 29 outliers final: 24 residues processed: 110 average time/residue: 0.1554 time to fit residues: 25.1978 Evaluate side-chains 113 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain A residue 83 THR 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 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 16 ASP 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 123 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 E residue 100 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 106 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 HIS G 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7637 Z= 0.427 Angle : 0.636 6.925 10409 Z= 0.336 Chirality : 0.051 0.159 1323 Planarity : 0.004 0.033 1337 Dihedral : 5.878 37.310 1043 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.05 % Allowed : 15.86 % 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: 0.07 (0.25), residues: 1001 helix: -3.57 (0.47), residues: 42 sheet: 0.64 (0.26), residues: 336 loop : 0.06 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 120 PHE 0.010 0.002 PHE D 40 TYR 0.011 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 121 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 85 time to evaluate : 0.810 Fit side-chains REVERT: A 72 MET cc_start: 0.7286 (mmm) cc_final: 0.6839 (mmm) REVERT: A 118 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.7931 (m) REVERT: C 126 THR cc_start: 0.8412 (m) cc_final: 0.8066 (p) REVERT: E 69 SER cc_start: 0.8574 (t) cc_final: 0.8333 (p) REVERT: E 122 ASP cc_start: 0.8435 (t0) cc_final: 0.8218 (t0) REVERT: E 139 LEU cc_start: 0.8266 (tp) cc_final: 0.7855 (mt) REVERT: F 87 LYS cc_start: 0.8015 (ptpp) cc_final: 0.7521 (ptpt) outliers start: 36 outliers final: 30 residues processed: 112 average time/residue: 0.1497 time to fit residues: 24.6021 Evaluate side-chains 116 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 85 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 112 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 138 SER 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 B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 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 123 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 E residue 100 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: 0.9980 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7812 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7637 Z= 0.181 Angle : 0.481 4.407 10409 Z= 0.258 Chirality : 0.045 0.143 1323 Planarity : 0.003 0.028 1337 Dihedral : 5.137 31.684 1043 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.37 % Allowed : 16.31 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1001 helix: -3.53 (0.48), residues: 42 sheet: 0.35 (0.26), residues: 364 loop : 0.44 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.005 0.001 PHE E 96 TYR 0.004 0.001 TYR G 133 ARG 0.001 0.000 ARG D 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 116 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 0.791 Fit side-chains REVERT: G 6 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8521 (m) REVERT: G 14 LYS cc_start: 0.7295 (mttm) cc_final: 0.6853 (mtpt) REVERT: G 138 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.8010 (m) REVERT: A 72 MET cc_start: 0.7195 (mmm) cc_final: 0.6735 (mmm) REVERT: A 118 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.7828 (m) REVERT: C 126 THR cc_start: 0.8300 (m) cc_final: 0.7950 (p) REVERT: E 32 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8595 (p) REVERT: E 69 SER cc_start: 0.8626 (t) cc_final: 0.8359 (p) REVERT: F 87 LYS cc_start: 0.8026 (ptpp) cc_final: 0.7534 (ptpt) outliers start: 30 outliers final: 25 residues processed: 111 average time/residue: 0.1417 time to fit residues: 23.2537 Evaluate side-chains 113 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 84 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain G residue 138 SER 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 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain D residue 16 ASP 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 123 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 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: 0.2980 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN B 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7637 Z= 0.169 Angle : 0.466 4.154 10409 Z= 0.249 Chirality : 0.044 0.142 1323 Planarity : 0.003 0.027 1337 Dihedral : 4.736 21.573 1043 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.26 % Allowed : 16.65 % 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: 0.36 (0.26), residues: 1001 helix: -3.43 (0.50), residues: 42 sheet: 0.46 (0.26), residues: 364 loop : 0.53 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.005 0.001 PHE E 96 TYR 0.003 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 114 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.830 Fit side-chains REVERT: G 6 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8522 (m) REVERT: G 14 LYS cc_start: 0.7295 (mttm) cc_final: 0.6855 (mtpt) REVERT: G 138 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.8009 (m) REVERT: A 72 MET cc_start: 0.7189 (mmm) cc_final: 0.6733 (mmm) REVERT: A 118 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7846 (m) REVERT: C 126 THR cc_start: 0.8316 (m) cc_final: 0.8035 (p) REVERT: E 69 SER cc_start: 0.8590 (t) cc_final: 0.8339 (p) outliers start: 29 outliers final: 25 residues processed: 108 average time/residue: 0.1611 time to fit residues: 25.5177 Evaluate side-chains 112 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain G residue 138 SER 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 C residue 6 THR Chi-restraints excluded: chain D residue 16 ASP 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 123 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 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 106 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 0.0470 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- 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 = 0.3096 r_free = 0.3096 target = 0.109579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.101589 restraints weight = 8836.998| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 0.94 r_work: 0.2911 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7637 Z= 0.308 Angle : 0.557 6.486 10409 Z= 0.294 Chirality : 0.047 0.152 1323 Planarity : 0.003 0.030 1337 Dihedral : 5.251 26.503 1043 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.37 % Allowed : 16.65 % Favored : 79.98 % 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: 0.20 (0.25), residues: 1001 helix: -3.49 (0.48), residues: 42 sheet: 0.68 (0.27), residues: 329 loop : 0.18 (0.24), 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 0.007 0.001 TYR E 133 ARG 0.002 0.000 ARG A 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1636.18 seconds wall clock time: 30 minutes 9.45 seconds (1809.45 seconds total)