Starting phenix.real_space_refine on Wed Mar 12 06:03:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ehs_28151/03_2025/8ehs_28151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehs_28151/03_2025/8ehs_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/cci-nas-00/data/ceres_data/8ehs_28151/03_2025/8ehs_28151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehs_28151/03_2025/8ehs_28151.map" model { file = "/net/cci-nas-00/data/ceres_data/8ehs_28151/03_2025/8ehs_28151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehs_28151/03_2025/8ehs_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-5624/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: 4.51, per 1000 atoms: 0.60 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: 1.55 Conformation dependent library (CDL) restraints added in 962.4 milliseconds 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: 1.47 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: 2.64 Time building geometry restraints manager: 1.88 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: 0.01 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: 0.330 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.070 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.743 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: 0.1912 time to fit residues: 30.5218 Evaluate side-chains 92 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.118297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.111244 restraints weight = 8575.512| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 0.82 r_work: 0.3059 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.680 Fit side-chains REVERT: G 39 ASN cc_start: 0.8791 (t0) cc_final: 0.8537 (t0) REVERT: G 69 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8556 (t) REVERT: G 141 MET cc_start: 0.8746 (mtm) cc_final: 0.8297 (mtp) REVERT: C 52 ASN cc_start: 0.7634 (t0) cc_final: 0.7304 (t0) REVERT: C 126 THR cc_start: 0.8202 (m) cc_final: 0.7708 (p) REVERT: C 141 MET cc_start: 0.9086 (ttp) cc_final: 0.8617 (mtm) outliers start: 11 outliers final: 9 residues processed: 118 average time/residue: 0.1830 time to fit residues: 29.7478 Evaluate side-chains 96 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 93 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.112665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.105280 restraints weight = 8925.180| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 0.88 r_work: 0.2974 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7637 Z= 0.368 Angle : 0.619 6.363 10409 Z= 0.329 Chirality : 0.050 0.163 1323 Planarity : 0.004 0.033 1337 Dihedral : 7.002 75.757 1043 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.14 % Allowed : 10.69 % Favored : 87.18 % 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: 0.53 (0.25), residues: 1001 helix: -3.77 (0.42), residues: 42 sheet: 1.03 (0.26), residues: 336 loop : 0.37 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 120 PHE 0.012 0.002 PHE D 40 TYR 0.007 0.002 TYR E 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 114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.772 Fit side-chains REVERT: A 142 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8120 (p) REVERT: C 72 MET cc_start: 0.8411 (mmm) cc_final: 0.8197 (mmm) REVERT: C 126 THR cc_start: 0.8277 (m) cc_final: 0.7859 (p) REVERT: E 69 SER cc_start: 0.8817 (t) cc_final: 0.8496 (p) REVERT: E 122 ASP cc_start: 0.8614 (t0) cc_final: 0.8394 (t0) REVERT: F 24 SER cc_start: 0.8727 (p) cc_final: 0.8270 (t) REVERT: F 87 LYS cc_start: 0.8189 (ptpp) cc_final: 0.7699 (ptpt) REVERT: F 129 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7394 (mp0) outliers start: 19 outliers final: 17 residues processed: 108 average time/residue: 0.1673 time to fit residues: 25.6880 Evaluate side-chains 108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 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 98 VAL 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 A residue 142 THR 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 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 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 81 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.114876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.107559 restraints weight = 8868.192| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 0.87 r_work: 0.3014 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2824 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= 0.211 Angle : 0.505 4.685 10409 Z= 0.271 Chirality : 0.046 0.151 1323 Planarity : 0.003 0.029 1337 Dihedral : 6.223 75.373 1043 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.71 % Allowed : 12.37 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1001 helix: -3.65 (0.45), residues: 42 sheet: 1.02 (0.27), residues: 329 loop : 0.38 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.006 0.001 PHE D 40 TYR 0.005 0.001 TYR G 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 123 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.749 Fit side-chains REVERT: G 138 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8236 (m) REVERT: A 72 MET cc_start: 0.7695 (mmm) cc_final: 0.7376 (mmm) REVERT: A 118 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.7905 (m) REVERT: A 142 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.8117 (p) REVERT: B 72 MET cc_start: 0.7756 (mmm) cc_final: 0.7525 (mmm) REVERT: C 126 THR cc_start: 0.8302 (m) cc_final: 0.7840 (p) REVERT: D 39 ASN cc_start: 0.9118 (t0) cc_final: 0.8850 (t0) REVERT: E 69 SER cc_start: 0.8891 (t) cc_final: 0.8603 (p) REVERT: F 87 LYS cc_start: 0.8203 (ptpp) cc_final: 0.7693 (ptpt) REVERT: F 129 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7297 (mp0) outliers start: 33 outliers final: 25 residues processed: 112 average time/residue: 0.1588 time to fit residues: 25.5095 Evaluate side-chains 114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 A residue 142 THR 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 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 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 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 10 SER 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 5 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 44 optimal weight: 0.0070 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN F 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.108196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.099937 restraints weight = 8982.182| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 0.98 r_work: 0.2892 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 7637 Z= 0.383 Angle : 0.608 6.015 10409 Z= 0.323 Chirality : 0.050 0.158 1323 Planarity : 0.004 0.036 1337 Dihedral : 6.622 84.362 1043 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.50 % Allowed : 13.05 % Favored : 82.45 % 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: -3.64 (0.45), residues: 42 sheet: 0.74 (0.26), residues: 336 loop : 0.15 (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 0.007 0.002 TYR E 133 ARG 0.002 0.000 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 129 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 0.786 Fit side-chains REVERT: A 118 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8002 (m) REVERT: A 142 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8121 (p) REVERT: C 126 THR cc_start: 0.8466 (m) cc_final: 0.8027 (p) REVERT: E 69 SER cc_start: 0.8835 (t) cc_final: 0.8576 (p) REVERT: E 122 ASP cc_start: 0.8646 (t0) cc_final: 0.8421 (t0) REVERT: F 24 SER cc_start: 0.8768 (p) cc_final: 0.8295 (t) REVERT: F 87 LYS cc_start: 0.8193 (ptpp) cc_final: 0.7682 (ptpt) REVERT: F 129 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7519 (mp0) outliers start: 40 outliers final: 32 residues processed: 117 average time/residue: 0.1496 time to fit residues: 25.3712 Evaluate side-chains 120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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 A residue 142 THR 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 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 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 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 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 65 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 0.0770 chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.115751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.108603 restraints weight = 8749.771| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 0.84 r_work: 0.3019 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7637 Z= 0.155 Angle : 0.462 4.545 10409 Z= 0.248 Chirality : 0.044 0.142 1323 Planarity : 0.003 0.028 1337 Dihedral : 5.831 87.536 1043 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.49 % Allowed : 15.19 % Favored : 81.33 % 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: 0.30 (0.26), residues: 1001 helix: -3.55 (0.47), residues: 42 sheet: 0.39 (0.26), residues: 357 loop : 0.51 (0.25), residues: 602 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 0.004 0.001 TYR G 133 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 118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.780 Fit side-chains REVERT: G 14 LYS cc_start: 0.7175 (mttm) cc_final: 0.6627 (mtpt) REVERT: G 118 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7992 (m) REVERT: G 138 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8248 (m) REVERT: A 72 MET cc_start: 0.7781 (mmm) cc_final: 0.7440 (mmm) REVERT: A 118 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.7944 (m) REVERT: C 126 THR cc_start: 0.8251 (m) cc_final: 0.7815 (p) REVERT: E 69 SER cc_start: 0.8832 (t) cc_final: 0.8610 (p) REVERT: F 87 LYS cc_start: 0.8211 (ptpp) cc_final: 0.7695 (ptpt) REVERT: F 129 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7267 (mp0) outliers start: 31 outliers final: 23 residues processed: 110 average time/residue: 0.1596 time to fit residues: 25.5330 Evaluate side-chains 111 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 118 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 44 SER Chi-restraints excluded: chain B residue 83 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 68 optimal weight: 0.0470 chunk 96 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 overall best weight: 0.8680 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.117754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.110819 restraints weight = 8632.986| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 0.79 r_work: 0.3052 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7637 Z= 0.137 Angle : 0.443 4.006 10409 Z= 0.238 Chirality : 0.044 0.142 1323 Planarity : 0.003 0.025 1337 Dihedral : 5.442 88.498 1043 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.92 % Allowed : 16.76 % 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: 0.54 (0.26), residues: 1001 helix: -3.46 (0.50), residues: 42 sheet: 0.59 (0.26), residues: 364 loop : 0.66 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.005 0.001 PHE E 96 TYR 0.003 0.001 TYR A 33 ARG 0.001 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 112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.840 Fit side-chains REVERT: G 14 LYS cc_start: 0.7203 (mttm) cc_final: 0.6648 (mtpt) REVERT: G 118 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7975 (m) REVERT: G 138 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8267 (m) REVERT: A 72 MET cc_start: 0.7715 (mmm) cc_final: 0.7317 (mmm) REVERT: A 118 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.7939 (m) REVERT: C 126 THR cc_start: 0.8191 (m) cc_final: 0.7750 (p) REVERT: D 39 ASN cc_start: 0.9051 (t0) cc_final: 0.8791 (t0) REVERT: E 6 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8604 (m) REVERT: F 129 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7199 (mp0) outliers start: 26 outliers final: 19 residues processed: 105 average time/residue: 0.1505 time to fit residues: 23.4111 Evaluate side-chains 108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 138 SER 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 91 THR 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 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 6 THR Chi-restraints excluded: chain F residue 16 ASP 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 89 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.0270 chunk 42 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 = 0.3194 r_free = 0.3194 target = 0.116950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.109807 restraints weight = 8783.384| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 0.84 r_work: 0.3036 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7637 Z= 0.164 Angle : 0.460 4.188 10409 Z= 0.244 Chirality : 0.044 0.142 1323 Planarity : 0.003 0.025 1337 Dihedral : 5.267 80.068 1043 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: 0.49 (0.26), residues: 1001 helix: -3.42 (0.50), residues: 42 sheet: 0.47 (0.26), residues: 357 loop : 0.69 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.006 0.001 PHE E 96 TYR 0.003 0.001 TYR G 133 ARG 0.001 0.000 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 113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.808 Fit side-chains REVERT: G 14 LYS cc_start: 0.7183 (mttm) cc_final: 0.6504 (mtpt) REVERT: G 118 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7982 (m) REVERT: G 138 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8277 (m) REVERT: A 72 MET cc_start: 0.7770 (mmm) cc_final: 0.7331 (mmm) REVERT: A 118 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.7928 (m) REVERT: C 126 THR cc_start: 0.8224 (m) cc_final: 0.7769 (p) REVERT: D 39 ASN cc_start: 0.9037 (t0) cc_final: 0.8775 (t0) REVERT: E 32 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8671 (p) REVERT: F 129 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7207 (mp0) outliers start: 29 outliers final: 22 residues processed: 109 average time/residue: 0.1423 time to fit residues: 23.0309 Evaluate side-chains 108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 138 SER 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 91 THR Chi-restraints excluded: chain B residue 118 THR 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 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 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 46 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 = 0.109613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.102517 restraints weight = 9030.867| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 0.83 r_work: 0.2983 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3262 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= 0.290 Angle : 0.543 6.206 10409 Z= 0.287 Chirality : 0.047 0.150 1323 Planarity : 0.003 0.027 1337 Dihedral : 5.563 65.714 1043 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.60 % Allowed : 16.54 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1001 helix: -3.47 (0.49), residues: 42 sheet: 0.66 (0.27), residues: 322 loop : 0.35 (0.24), residues: 637 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 0.005 0.001 TYR F 133 ARG 0.002 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 121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.811 Fit side-chains REVERT: G 14 LYS cc_start: 0.7231 (mttm) cc_final: 0.6635 (mtpt) REVERT: A 72 MET cc_start: 0.7917 (mmm) cc_final: 0.7486 (mmm) REVERT: A 118 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.7964 (m) REVERT: C 126 THR cc_start: 0.8400 (m) cc_final: 0.7994 (p) REVERT: E 32 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8661 (p) REVERT: E 122 ASP cc_start: 0.8600 (t0) cc_final: 0.8353 (t0) REVERT: F 87 LYS cc_start: 0.8250 (ptpp) cc_final: 0.7731 (ptpt) REVERT: F 129 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7276 (mp0) outliers start: 32 outliers final: 29 residues processed: 114 average time/residue: 0.1492 time to fit residues: 24.8280 Evaluate side-chains 119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 100 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 6 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 63 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.114561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.106885 restraints weight = 8810.965| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 0.88 r_work: 0.3000 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3256 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= 0.218 Angle : 0.494 4.317 10409 Z= 0.264 Chirality : 0.045 0.145 1323 Planarity : 0.003 0.028 1337 Dihedral : 5.307 57.361 1043 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.49 % Allowed : 16.76 % Favored : 79.75 % 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: 0.28 (0.26), residues: 1001 helix: -3.43 (0.49), residues: 42 sheet: 0.27 (0.26), residues: 357 loop : 0.56 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.006 0.001 PHE E 96 TYR 0.004 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 118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.831 Fit side-chains REVERT: G 14 LYS cc_start: 0.7232 (mttm) cc_final: 0.6630 (mtpt) REVERT: G 138 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8230 (m) REVERT: A 72 MET cc_start: 0.7874 (mmm) cc_final: 0.7432 (mmm) REVERT: A 118 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.7934 (m) REVERT: C 126 THR cc_start: 0.8448 (m) cc_final: 0.7981 (p) REVERT: E 32 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8681 (p) REVERT: F 87 LYS cc_start: 0.8212 (ptpp) cc_final: 0.7680 (ptpt) REVERT: F 129 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7236 (mp0) outliers start: 31 outliers final: 28 residues processed: 110 average time/residue: 0.1538 time to fit residues: 24.6817 Evaluate side-chains 118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 6 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.108873 restraints weight = 8806.242| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 0.84 r_work: 0.3026 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 0.026 7637 Z= 0.173 Angle : 0.468 4.099 10409 Z= 0.249 Chirality : 0.044 0.141 1323 Planarity : 0.003 0.026 1337 Dihedral : 4.942 46.967 1043 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.49 % Allowed : 16.87 % Favored : 79.64 % 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: 0.37 (0.26), residues: 1001 helix: -3.39 (0.50), residues: 42 sheet: 0.34 (0.26), residues: 357 loop : 0.62 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.006 0.001 PHE E 96 TYR 0.004 0.001 TYR G 133 ARG 0.001 0.000 ARG D 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3266.91 seconds wall clock time: 57 minutes 11.83 seconds (3431.83 seconds total)