Starting phenix.real_space_refine on Sun May 11 03:15:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ehs_28151/05_2025/8ehs_28151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehs_28151/05_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_28151/05_2025/8ehs_28151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehs_28151/05_2025/8ehs_28151.map" model { file = "/net/cci-nas-00/data/ceres_data/8ehs_28151/05_2025/8ehs_28151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehs_28151/05_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-5687/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: 4.61, per 1000 atoms: 0.61 Number of scatterers: 7546 At special positions: 0 Unit cell: (85.162, 85.162, 99.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1596 8.00 N 1253 7.00 C 4676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.58 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: 1.22 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: 2.08 Time building geometry restraints manager: 1.89 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.860 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- 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= 0.135 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 Details of bonding type rmsd hydrogen bonds : bond 0.25447 ( 261) hydrogen bonds : angle 10.46862 ( 762) covalent geometry : bond 0.00233 ( 7637) covalent geometry : angle 0.47127 (10409) *********************** 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 : 0.860 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: 0.1942 time to fit residues: 31.0982 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 : 0.864 ------------------------------------------------------------------------------- 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 = 8575.513| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 0.82 r_work: 0.3060 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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= 0.161 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 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 261) hydrogen bonds : angle 5.71128 ( 762) covalent geometry : bond 0.00390 ( 7637) covalent geometry : angle 0.57118 (10409) *********************** 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 : 0.762 Fit side-chains REVERT: G 39 ASN cc_start: 0.8797 (t0) cc_final: 0.8544 (t0) REVERT: G 69 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8560 (t) REVERT: G 141 MET cc_start: 0.8744 (mtm) cc_final: 0.8298 (mtp) REVERT: C 52 ASN cc_start: 0.7632 (t0) cc_final: 0.7302 (t0) REVERT: C 126 THR cc_start: 0.8203 (m) cc_final: 0.7712 (p) REVERT: C 141 MET cc_start: 0.9084 (ttp) cc_final: 0.8617 (mtm) outliers start: 11 outliers final: 9 residues processed: 118 average time/residue: 0.1790 time to fit residues: 28.9427 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 : 0.754 ------------------------------------------------------------------------------- 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: 7.9990 chunk 34 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.113803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.106766 restraints weight = 8880.006| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 0.80 r_work: 0.2997 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7637 Z= 0.189 Angle : 0.580 5.819 10409 Z= 0.310 Chirality : 0.049 0.160 1323 Planarity : 0.003 0.031 1337 Dihedral : 6.792 73.055 1043 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.91 % Allowed : 10.80 % Favored : 87.29 % 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 (0.25), residues: 1001 helix: -3.74 (0.42), residues: 42 sheet: 0.84 (0.26), residues: 350 loop : 0.37 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.010 0.001 PHE D 40 TYR 0.005 0.002 TYR F 133 ARG 0.002 0.001 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 261) hydrogen bonds : angle 5.50340 ( 762) covalent geometry : bond 0.00475 ( 7637) covalent geometry : angle 0.58034 (10409) *********************** 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 111 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.792 Fit side-chains REVERT: C 72 MET cc_start: 0.8363 (mmm) cc_final: 0.8129 (mmm) REVERT: C 126 THR cc_start: 0.8258 (m) cc_final: 0.7847 (p) REVERT: E 69 SER cc_start: 0.8812 (t) cc_final: 0.8499 (p) REVERT: E 122 ASP cc_start: 0.8608 (t0) cc_final: 0.8353 (t0) REVERT: F 24 SER cc_start: 0.8719 (p) cc_final: 0.8262 (t) REVERT: F 87 LYS cc_start: 0.8256 (ptpp) cc_final: 0.7763 (ptpt) REVERT: F 129 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7375 (mp0) outliers start: 17 outliers final: 16 residues processed: 106 average time/residue: 0.1705 time to fit residues: 25.4561 Evaluate side-chains 106 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 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 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.113442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.106579 restraints weight = 8883.056| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 0.79 r_work: 0.2994 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2902 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= 0.173 Angle : 0.551 5.170 10409 Z= 0.295 Chirality : 0.048 0.154 1323 Planarity : 0.003 0.032 1337 Dihedral : 6.340 74.624 1043 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.71 % Allowed : 12.60 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1001 helix: -3.63 (0.46), residues: 42 sheet: 0.93 (0.27), residues: 329 loop : 0.33 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 120 PHE 0.008 0.001 PHE D 40 TYR 0.006 0.001 TYR G 133 ARG 0.002 0.001 ARG D 8 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 261) hydrogen bonds : angle 5.37297 ( 762) covalent geometry : bond 0.00436 ( 7637) covalent geometry : angle 0.55098 (10409) *********************** 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 to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.769 Fit side-chains REVERT: G 138 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8217 (m) REVERT: A 72 MET cc_start: 0.7745 (mmm) cc_final: 0.7427 (mmm) REVERT: A 118 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.7956 (m) REVERT: C 126 THR cc_start: 0.8320 (m) cc_final: 0.7933 (p) REVERT: D 39 ASN cc_start: 0.9135 (t0) cc_final: 0.8886 (t0) REVERT: E 69 SER cc_start: 0.8833 (t) cc_final: 0.8568 (p) REVERT: E 122 ASP cc_start: 0.8643 (t0) cc_final: 0.8406 (t0) REVERT: F 87 LYS cc_start: 0.8235 (ptpp) cc_final: 0.7736 (ptpt) REVERT: F 129 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7328 (mp0) outliers start: 33 outliers final: 25 residues processed: 114 average time/residue: 0.1566 time to fit residues: 25.4648 Evaluate side-chains 113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 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 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 28 SER Chi-restraints excluded: chain E residue 32 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: 5.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 B 50 HIS F 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.106317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.098634 restraints weight = 9045.680| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 0.90 r_work: 0.2878 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 7637 Z= 0.278 Angle : 0.668 6.712 10409 Z= 0.354 Chirality : 0.052 0.164 1323 Planarity : 0.004 0.041 1337 Dihedral : 6.957 89.593 1043 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.72 % Allowed : 13.27 % Favored : 82.00 % 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: -0.03 (0.25), residues: 1001 helix: -3.75 (0.42), residues: 42 sheet: 0.57 (0.26), residues: 336 loop : -0.01 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 120 PHE 0.011 0.002 PHE D 40 TYR 0.010 0.002 TYR E 133 ARG 0.003 0.001 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 261) hydrogen bonds : angle 5.72120 ( 762) covalent geometry : bond 0.00708 ( 7637) covalent geometry : angle 0.66758 (10409) *********************** 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 127 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.775 Fit side-chains REVERT: A 118 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8031 (m) REVERT: C 126 THR cc_start: 0.8440 (m) cc_final: 0.8022 (p) REVERT: E 69 SER cc_start: 0.8830 (t) cc_final: 0.8558 (p) REVERT: E 139 LEU cc_start: 0.8338 (tp) cc_final: 0.7943 (mt) REVERT: F 24 SER cc_start: 0.8780 (p) cc_final: 0.8333 (t) REVERT: F 87 LYS cc_start: 0.8216 (ptpp) cc_final: 0.7716 (ptpt) REVERT: F 129 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7575 (mp0) outliers start: 42 outliers final: 34 residues processed: 115 average time/residue: 0.1463 time to fit residues: 24.7073 Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER 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 118 THR 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 118 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 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 97 THR Chi-restraints excluded: chain D residue 100 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 6 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 65 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3199 r_free = 0.3199 target = 0.117286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.110340 restraints weight = 8700.626| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 0.79 r_work: 0.3042 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7637 Z= 0.087 Angle : 0.454 3.450 10409 Z= 0.245 Chirality : 0.044 0.140 1323 Planarity : 0.003 0.029 1337 Dihedral : 5.764 86.326 1043 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.04 % Allowed : 15.86 % Favored : 81.10 % 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: -3.62 (0.45), residues: 42 sheet: 0.33 (0.26), residues: 357 loop : 0.43 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 120 PHE 0.006 0.001 PHE E 96 TYR 0.003 0.000 TYR B 133 ARG 0.001 0.000 ARG D 8 Details of bonding type rmsd hydrogen bonds : bond 0.02525 ( 261) hydrogen bonds : angle 5.02839 ( 762) covalent geometry : bond 0.00202 ( 7637) covalent geometry : angle 0.45396 (10409) *********************** 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 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.737 Fit side-chains REVERT: G 14 LYS cc_start: 0.7127 (mttm) cc_final: 0.6580 (mtpt) REVERT: G 69 SER cc_start: 0.8833 (p) cc_final: 0.8467 (t) REVERT: G 138 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8246 (m) REVERT: C 52 ASN cc_start: 0.7802 (t0) cc_final: 0.7445 (t0) REVERT: C 126 THR cc_start: 0.8330 (m) cc_final: 0.7872 (p) REVERT: C 141 MET cc_start: 0.8982 (ttp) cc_final: 0.8447 (mtm) REVERT: E 69 SER cc_start: 0.8803 (t) cc_final: 0.8594 (p) REVERT: F 87 LYS cc_start: 0.8177 (ptpp) cc_final: 0.7676 (ptpt) REVERT: F 129 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7237 (mp0) outliers start: 27 outliers final: 20 residues processed: 110 average time/residue: 0.1451 time to fit residues: 23.4921 Evaluate side-chains 107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 83 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 100 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 106 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 23 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 77 optimal weight: 0.0170 chunk 5 optimal weight: 7.9990 chunk 80 optimal weight: 0.4980 chunk 68 optimal weight: 0.0020 chunk 96 optimal weight: 0.0770 chunk 43 optimal weight: 0.8980 overall best weight: 0.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN E 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.123629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.116859 restraints weight = 8567.920| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 0.77 r_work: 0.3124 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7637 Z= 0.071 Angle : 0.414 3.411 10409 Z= 0.222 Chirality : 0.043 0.135 1323 Planarity : 0.003 0.024 1337 Dihedral : 4.799 81.160 1043 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.91 % Allowed : 17.77 % 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: 0.63 (0.26), residues: 1001 helix: -3.47 (0.50), residues: 42 sheet: 0.72 (0.26), residues: 364 loop : 0.68 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.005 0.001 PHE B 40 TYR 0.004 0.001 TYR E 133 ARG 0.001 0.000 ARG D 8 Details of bonding type rmsd hydrogen bonds : bond 0.02270 ( 261) hydrogen bonds : angle 4.50755 ( 762) covalent geometry : bond 0.00158 ( 7637) covalent geometry : angle 0.41364 (10409) *********************** 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: 17 poor density : 95 time to evaluate : 0.823 Fit side-chains REVERT: G 14 LYS cc_start: 0.7209 (mttm) cc_final: 0.6599 (mtpt) REVERT: G 69 SER cc_start: 0.8786 (p) cc_final: 0.8474 (t) REVERT: G 72 MET cc_start: 0.7400 (mmt) cc_final: 0.6024 (mtt) REVERT: A 118 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.7877 (m) REVERT: C 126 THR cc_start: 0.8000 (m) cc_final: 0.7664 (p) REVERT: C 141 MET cc_start: 0.8971 (ttp) cc_final: 0.8533 (mtm) REVERT: D 47 THR cc_start: 0.8929 (p) cc_final: 0.8660 (p) REVERT: E 6 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8608 (m) REVERT: E 56 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7822 (mttm) REVERT: F 115 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8080 (mm-40) REVERT: F 129 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7153 (mp0) outliers start: 17 outliers final: 10 residues processed: 109 average time/residue: 0.1396 time to fit residues: 22.6571 Evaluate side-chains 101 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 100 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 89 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN C 38 ASN D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.112890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.105341 restraints weight = 8892.423| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 0.88 r_work: 0.2976 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7637 Z= 0.194 Angle : 0.564 6.432 10409 Z= 0.298 Chirality : 0.047 0.150 1323 Planarity : 0.003 0.027 1337 Dihedral : 5.560 64.615 1043 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.60 % Allowed : 16.65 % 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: 0.31 (0.25), residues: 1001 helix: -3.54 (0.46), residues: 42 sheet: 0.73 (0.27), residues: 322 loop : 0.30 (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 E 96 TYR 0.009 0.002 TYR E 133 ARG 0.002 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 261) hydrogen bonds : angle 5.14404 ( 762) covalent geometry : bond 0.00485 ( 7637) covalent geometry : angle 0.56382 (10409) *********************** 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 118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.772 Fit side-chains REVERT: G 14 LYS cc_start: 0.7228 (mttm) cc_final: 0.6638 (mtpt) REVERT: A 118 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.7971 (m) REVERT: B 141 MET cc_start: 0.9026 (ttp) cc_final: 0.8814 (ttp) REVERT: C 126 THR cc_start: 0.8470 (m) cc_final: 0.8047 (p) REVERT: E 69 SER cc_start: 0.8787 (t) cc_final: 0.8574 (p) REVERT: F 87 LYS cc_start: 0.8225 (ptpp) cc_final: 0.7718 (ptpt) REVERT: F 129 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7407 (mp0) outliers start: 32 outliers final: 27 residues processed: 111 average time/residue: 0.1470 time to fit residues: 24.1000 Evaluate side-chains 113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 51 THR 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 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 123 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 123 THR Chi-restraints excluded: chain F residue 6 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3145 r_free = 0.3145 target = 0.113163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.105701 restraints weight = 8942.061| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 0.86 r_work: 0.2979 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7637 Z= 0.168 Angle : 0.533 5.044 10409 Z= 0.284 Chirality : 0.047 0.148 1323 Planarity : 0.003 0.028 1337 Dihedral : 5.485 54.137 1043 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.04 % Allowed : 17.21 % 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: 0.19 (0.25), residues: 1001 helix: -3.52 (0.47), residues: 42 sheet: 0.60 (0.27), residues: 322 loop : 0.23 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.006 0.001 PHE E 96 TYR 0.006 0.001 TYR A 133 ARG 0.002 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.02890 ( 261) hydrogen bonds : angle 5.17999 ( 762) covalent geometry : bond 0.00426 ( 7637) covalent geometry : angle 0.53333 (10409) *********************** 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 111 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.781 Fit side-chains REVERT: G 14 LYS cc_start: 0.7213 (mttm) cc_final: 0.6626 (mtpt) REVERT: G 39 ASN cc_start: 0.8762 (t0) cc_final: 0.8528 (m-40) REVERT: A 118 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.7950 (m) REVERT: C 126 THR cc_start: 0.8420 (m) cc_final: 0.7974 (p) REVERT: E 32 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8608 (p) REVERT: E 69 SER cc_start: 0.8813 (t) cc_final: 0.8571 (p) REVERT: F 87 LYS cc_start: 0.8215 (ptpp) cc_final: 0.7708 (ptpt) REVERT: F 129 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7407 (mp0) outliers start: 27 outliers final: 23 residues processed: 103 average time/residue: 0.1602 time to fit residues: 23.8007 Evaluate side-chains 109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 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 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 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 123 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 = 0.3068 r_free = 0.3068 target = 0.107552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.099759 restraints weight = 9043.634| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 0.91 r_work: 0.2896 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7637 Z= 0.212 Angle : 0.591 5.774 10409 Z= 0.313 Chirality : 0.048 0.153 1323 Planarity : 0.004 0.033 1337 Dihedral : 5.739 44.655 1043 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.04 % Allowed : 17.10 % 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: -0.00 (0.25), residues: 1001 helix: -3.56 (0.47), residues: 42 sheet: 0.47 (0.26), residues: 329 loop : 0.09 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 120 PHE 0.008 0.001 PHE D 40 TYR 0.007 0.002 TYR E 133 ARG 0.002 0.001 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 261) hydrogen bonds : angle 5.34645 ( 762) covalent geometry : bond 0.00540 ( 7637) covalent geometry : angle 0.59063 (10409) ********************** 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 to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.778 Fit side-chains REVERT: A 118 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.7980 (m) REVERT: C 126 THR cc_start: 0.8522 (m) cc_final: 0.8075 (p) REVERT: E 32 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8645 (p) REVERT: E 69 SER cc_start: 0.8832 (t) cc_final: 0.8557 (p) REVERT: E 139 LEU cc_start: 0.8379 (tp) cc_final: 0.7970 (mt) REVERT: F 87 LYS cc_start: 0.8178 (ptpp) cc_final: 0.7663 (ptpt) REVERT: F 129 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7474 (mp0) outliers start: 27 outliers final: 25 residues processed: 105 average time/residue: 0.1582 time to fit residues: 24.0763 Evaluate side-chains 112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 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 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 32 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.116298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.109480 restraints weight = 8819.201| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 0.77 r_work: 0.3031 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7637 Z= 0.094 Angle : 0.463 4.031 10409 Z= 0.247 Chirality : 0.044 0.139 1323 Planarity : 0.003 0.028 1337 Dihedral : 4.914 33.061 1043 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.47 % Allowed : 18.00 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1001 helix: -3.53 (0.48), residues: 42 sheet: 0.20 (0.26), residues: 357 loop : 0.45 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 50 PHE 0.007 0.001 PHE E 96 TYR 0.005 0.001 TYR A 133 ARG 0.001 0.000 ARG D 8 Details of bonding type rmsd hydrogen bonds : bond 0.02453 ( 261) hydrogen bonds : angle 4.90755 ( 762) covalent geometry : bond 0.00229 ( 7637) covalent geometry : angle 0.46256 (10409) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.35 seconds wall clock time: 56 minutes 46.60 seconds (3406.60 seconds total)