Starting phenix.real_space_refine on Tue Sep 15 00:58:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10am_75029/09_2026/10am_75029.cif Found real_map, /net/cci-nas-00/data/ceres_data/10am_75029/09_2026/10am_75029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10am_75029/09_2026/10am_75029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10am_75029/09_2026/10am_75029.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10am_75029/09_2026/10am_75029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10am_75029/09_2026/10am_75029.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.020 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: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 10584 2.51 5 N 2745 2.21 5 O 3258 1.98 5 H 16920 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33525 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3725 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3725 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3725 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3725 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3725 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3725 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3725 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3725 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3725 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.84, per 1000 atoms: 0.17 Number of scatterers: 33525 At special positions: 0 Unit cell: (116.63, 116.63, 143.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 3258 8.00 N 2745 7.00 C 10584 6.00 H 16920 1.00 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: 3.40 Conformation dependent library (CDL) restraints added in 1.3 seconds 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 36 sheets defined 43.3% alpha, 48.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 removed outlier: 3.676A pdb=" N LEU A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 87 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 168 through 192 Processing helix chain 'B' and resid 5 through 33 removed outlier: 3.685A pdb=" N LEU B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 142 through 148 Processing helix chain 'B' and resid 168 through 192 Processing helix chain 'C' and resid 5 through 33 removed outlier: 3.678A pdb=" N LEU C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 87 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 168 through 192 Processing helix chain 'D' and resid 5 through 33 removed outlier: 3.683A pdb=" N LEU D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 87 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 130 through 141 Processing helix chain 'D' and resid 142 through 148 Processing helix chain 'D' and resid 168 through 192 Processing helix chain 'E' and resid 5 through 33 removed outlier: 3.689A pdb=" N LEU E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 87 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 142 through 148 Processing helix chain 'E' and resid 168 through 192 Processing helix chain 'F' and resid 5 through 33 removed outlier: 3.689A pdb=" N LEU F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 87 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 130 through 141 Processing helix chain 'F' and resid 142 through 148 Processing helix chain 'F' and resid 168 through 192 Processing helix chain 'G' and resid 5 through 33 removed outlier: 3.697A pdb=" N LEU G 33 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 87 Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 130 through 141 Processing helix chain 'G' and resid 142 through 148 Processing helix chain 'G' and resid 168 through 192 Processing helix chain 'H' and resid 5 through 33 removed outlier: 3.683A pdb=" N LEU H 33 " --> pdb=" O ASP H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 87 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 130 through 141 Processing helix chain 'H' and resid 142 through 148 Processing helix chain 'H' and resid 168 through 192 Processing helix chain 'I' and resid 5 through 33 removed outlier: 3.674A pdb=" N LEU I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 87 Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 130 through 141 Processing helix chain 'I' and resid 142 through 148 Processing helix chain 'I' and resid 168 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 48 removed outlier: 6.419A pdb=" N TYR A 230 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 198 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS A 232 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY A 196 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 removed outlier: 4.377A pdb=" N VAL A 150 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 48 removed outlier: 6.424A pdb=" N TYR B 230 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 198 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LYS B 232 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY B 196 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 48 Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 95 removed outlier: 4.396A pdb=" N VAL B 150 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 48 removed outlier: 6.362A pdb=" N TYR C 230 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 198 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS C 232 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY C 196 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 36 through 48 Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 95 removed outlier: 4.391A pdb=" N VAL C 150 " --> pdb=" O THR C 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 36 through 48 removed outlier: 6.373A pdb=" N TYR D 230 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE D 198 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS D 232 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY D 196 " --> pdb=" O LYS D 232 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 36 through 48 Processing sheet with id=AB6, first strand: chain 'D' and resid 93 through 95 removed outlier: 4.393A pdb=" N VAL D 150 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AB8, first strand: chain 'E' and resid 36 through 48 removed outlier: 6.391A pdb=" N TYR E 230 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE E 198 " --> pdb=" O TYR E 230 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS E 232 " --> pdb=" O GLY E 196 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY E 196 " --> pdb=" O LYS E 232 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 36 through 48 Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 95 removed outlier: 4.393A pdb=" N VAL E 150 " --> pdb=" O THR E 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AC3, first strand: chain 'F' and resid 36 through 48 removed outlier: 6.372A pdb=" N TYR F 230 " --> pdb=" O ILE F 198 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE F 198 " --> pdb=" O TYR F 230 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS F 232 " --> pdb=" O GLY F 196 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY F 196 " --> pdb=" O LYS F 232 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 36 through 48 Processing sheet with id=AC5, first strand: chain 'F' and resid 93 through 95 removed outlier: 4.382A pdb=" N VAL F 150 " --> pdb=" O THR F 59 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AC7, first strand: chain 'G' and resid 36 through 48 removed outlier: 6.389A pdb=" N TYR G 230 " --> pdb=" O ILE G 198 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE G 198 " --> pdb=" O TYR G 230 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS G 232 " --> pdb=" O GLY G 196 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY G 196 " --> pdb=" O LYS G 232 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 36 through 48 Processing sheet with id=AC9, first strand: chain 'G' and resid 93 through 95 removed outlier: 4.401A pdb=" N VAL G 150 " --> pdb=" O THR G 59 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AD2, first strand: chain 'H' and resid 36 through 48 removed outlier: 6.348A pdb=" N TYR H 230 " --> pdb=" O ILE H 198 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE H 198 " --> pdb=" O TYR H 230 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS H 232 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY H 196 " --> pdb=" O LYS H 232 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 36 through 48 Processing sheet with id=AD4, first strand: chain 'H' and resid 93 through 95 removed outlier: 4.356A pdb=" N VAL H 150 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AD6, first strand: chain 'I' and resid 36 through 48 removed outlier: 6.353A pdb=" N TYR I 230 " --> pdb=" O ILE I 198 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE I 198 " --> pdb=" O TYR I 230 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS I 232 " --> pdb=" O GLY I 196 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY I 196 " --> pdb=" O LYS I 232 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 36 through 48 Processing sheet with id=AD8, first strand: chain 'I' and resid 93 through 95 removed outlier: 4.331A pdb=" N VAL I 150 " --> pdb=" O THR I 59 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 101 through 102 1294 hydrogen bonds defined for protein. 3612 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: 8.36 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16920 1.03 - 1.22: 0 1.22 - 1.42: 6818 1.42 - 1.61: 9985 1.61 - 1.80: 36 Bond restraints: 33759 Sorted by residual: bond pdb=" N PRO C 55 " pdb=" CA PRO C 55 " ideal model delta sigma weight residual 1.469 1.483 -0.014 1.28e-02 6.10e+03 1.17e+00 bond pdb=" N PRO E 55 " pdb=" CA PRO E 55 " ideal model delta sigma weight residual 1.469 1.482 -0.014 1.28e-02 6.10e+03 1.12e+00 bond pdb=" N PRO B 55 " pdb=" CA PRO B 55 " ideal model delta sigma weight residual 1.469 1.482 -0.013 1.28e-02 6.10e+03 1.11e+00 bond pdb=" N PRO H 55 " pdb=" CA PRO H 55 " ideal model delta sigma weight residual 1.469 1.482 -0.013 1.28e-02 6.10e+03 1.08e+00 bond pdb=" N PRO G 55 " pdb=" CA PRO G 55 " ideal model delta sigma weight residual 1.469 1.482 -0.013 1.28e-02 6.10e+03 1.06e+00 ... (remaining 33754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 55089 0.83 - 1.67: 5654 1.67 - 2.50: 422 2.50 - 3.34: 17 3.34 - 4.17: 27 Bond angle restraints: 61209 Sorted by residual: angle pdb=" N ASP A 167 " pdb=" CA ASP A 167 " pdb=" C ASP A 167 " ideal model delta sigma weight residual 113.97 111.93 2.04 1.28e+00 6.10e-01 2.54e+00 angle pdb=" N ASP I 167 " pdb=" CA ASP I 167 " pdb=" C ASP I 167 " ideal model delta sigma weight residual 113.97 111.95 2.02 1.28e+00 6.10e-01 2.49e+00 angle pdb=" N ASP H 167 " pdb=" CA ASP H 167 " pdb=" C ASP H 167 " ideal model delta sigma weight residual 113.97 111.99 1.98 1.28e+00 6.10e-01 2.39e+00 angle pdb=" CA PRO C 55 " pdb=" C PRO C 55 " pdb=" O PRO C 55 " ideal model delta sigma weight residual 120.60 123.23 -2.63 1.82e+00 3.02e-01 2.09e+00 angle pdb=" CA PRO I 55 " pdb=" C PRO I 55 " pdb=" O PRO I 55 " ideal model delta sigma weight residual 120.60 123.22 -2.62 1.82e+00 3.02e-01 2.07e+00 ... (remaining 61204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.74: 14059 11.74 - 23.47: 1348 23.47 - 35.20: 218 35.20 - 46.94: 70 46.94 - 58.67: 64 Dihedral angle restraints: 15759 sinusoidal: 8703 harmonic: 7056 Sorted by residual: dihedral pdb=" N ARG F 222 " pdb=" CA ARG F 222 " pdb=" CB ARG F 222 " pdb=" CG ARG F 222 " ideal model delta sinusoidal sigma weight residual -60.00 -118.67 58.67 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ARG C 222 " pdb=" CA ARG C 222 " pdb=" CB ARG C 222 " pdb=" CG ARG C 222 " ideal model delta sinusoidal sigma weight residual -60.00 -118.46 58.46 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ARG I 222 " pdb=" CA ARG I 222 " pdb=" CB ARG I 222 " pdb=" CG ARG I 222 " ideal model delta sinusoidal sigma weight residual -60.00 -118.14 58.14 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 15756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1620 0.028 - 0.056: 685 0.056 - 0.084: 116 0.084 - 0.113: 143 0.113 - 0.141: 91 Chirality restraints: 2655 Sorted by residual: chirality pdb=" CA ILE G 218 " pdb=" N ILE G 218 " pdb=" C ILE G 218 " pdb=" CB ILE G 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE A 218 " pdb=" N ILE A 218 " pdb=" C ILE A 218 " pdb=" CB ILE A 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE D 218 " pdb=" N ILE D 218 " pdb=" C ILE D 218 " pdb=" CB ILE D 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 2652 not shown) Planarity restraints: 4923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 54 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO H 55 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 55 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 55 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 54 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO E 55 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 54 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.28e+00 pdb=" N PRO C 55 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.025 5.00e-02 4.00e+02 ... (remaining 4920 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.47: 21851 2.47 - 3.00: 76427 3.00 - 3.53: 84779 3.53 - 4.07: 109747 4.07 - 4.60: 163199 Nonbonded interactions: 456003 Sorted by model distance: nonbonded pdb="HE22 GLN G 86 " pdb="HD22 ASN G 140 " model vdw 1.932 2.100 nonbonded pdb=" H SER H 142 " pdb=" HG SER I 97 " model vdw 1.935 2.100 nonbonded pdb="HE22 GLN H 86 " pdb="HD22 ASN H 140 " model vdw 1.936 2.100 nonbonded pdb="HE22 GLN D 86 " pdb="HD22 ASN D 140 " model vdw 1.937 2.100 nonbonded pdb="HE22 GLN I 86 " pdb="HD22 ASN I 140 " model vdw 1.937 2.100 ... (remaining 455998 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: 0.08 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' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.210 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 33.180 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.003 0.022 16839 Z= 0.144 Angle : 0.440 4.172 22734 Z= 0.253 Chirality : 0.043 0.141 2655 Planarity : 0.003 0.047 2898 Dihedral : 9.166 58.675 6390 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.49 % Allowed : 2.27 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.19), residues: 2061 helix: 3.49 (0.17), residues: 855 sheet: -0.50 (0.19), residues: 621 loop : 0.10 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 35 TYR 0.008 0.001 TYR D 230 PHE 0.008 0.001 PHE F 58 HIS 0.001 0.000 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (16839) covalent geometry : angle 0.43968 / 0.25 (22734) hydrogen bonds : bond 0.19330 / 13.01 ( 1078) hydrogen bonds : angle 7.46716 / 5.29 ( 3612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 366 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.8032 (m-30) cc_final: 0.7728 (m-30) REVERT: A 200 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8556 (mtmt) REVERT: A 203 GLN cc_start: 0.8604 (tp40) cc_final: 0.8234 (mm-40) REVERT: B 200 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8506 (mtmm) REVERT: C 203 GLN cc_start: 0.8638 (tp40) cc_final: 0.8204 (mm-40) REVERT: E 203 GLN cc_start: 0.8693 (tp40) cc_final: 0.8341 (mm-40) REVERT: F 157 ASP cc_start: 0.8098 (m-30) cc_final: 0.7815 (m-30) REVERT: F 203 GLN cc_start: 0.8592 (tp40) cc_final: 0.8234 (mm-40) REVERT: G 203 GLN cc_start: 0.8553 (tp40) cc_final: 0.8246 (mm-40) REVERT: H 157 ASP cc_start: 0.8085 (m-30) cc_final: 0.7787 (m-30) REVERT: I 157 ASP cc_start: 0.8065 (m-30) cc_final: 0.7821 (m-30) REVERT: I 203 GLN cc_start: 0.8631 (tp40) cc_final: 0.8280 (mm-40) outliers start: 9 outliers final: 0 residues processed: 375 average time/residue: 0.3208 time to fit residues: 174.2286 Evaluate side-chains 211 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN C 203 GLN E 203 GLN F 203 GLN G 4 ASN G 113 GLN G 203 GLN I 203 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.067873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056353 restraints weight = 137645.661| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.21 r_work: 0.2690 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16839 Z= 0.176 Angle : 0.511 4.232 22734 Z= 0.291 Chirality : 0.043 0.149 2655 Planarity : 0.005 0.063 2898 Dihedral : 3.580 11.917 2250 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.43 % Allowed : 5.23 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.19), residues: 2061 helix: 3.34 (0.17), residues: 864 sheet: -0.05 (0.20), residues: 612 loop : 0.30 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 60 TYR 0.008 0.001 TYR F 229 PHE 0.008 0.001 PHE E 58 HIS 0.001 0.000 HIS G 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (16839) covalent geometry : angle 0.51085 / 0.29 (22734) hydrogen bonds : bond 0.04964 / 3.38 ( 1078) hydrogen bonds : angle 5.28287 / 3.72 ( 3612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 210 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8390 (tp40) cc_final: 0.8031 (pm20) REVERT: A 157 ASP cc_start: 0.8812 (m-30) cc_final: 0.8585 (m-30) REVERT: A 203 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8496 (mm-40) REVERT: C 161 LEU cc_start: 0.9274 (mt) cc_final: 0.9007 (mt) REVERT: C 203 GLN cc_start: 0.8731 (tp-100) cc_final: 0.8341 (mm-40) REVERT: C 222 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8259 (mtt-85) REVERT: E 203 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8339 (mm-40) REVERT: F 157 ASP cc_start: 0.8768 (m-30) cc_final: 0.8540 (m-30) REVERT: F 203 GLN cc_start: 0.8728 (tp-100) cc_final: 0.8356 (mm-40) REVERT: F 222 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8303 (ttm110) REVERT: G 203 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8484 (mm-40) REVERT: H 113 GLN cc_start: 0.8373 (tp40) cc_final: 0.7881 (pm20) REVERT: H 157 ASP cc_start: 0.8795 (m-30) cc_final: 0.8352 (m-30) REVERT: I 157 ASP cc_start: 0.8850 (m-30) cc_final: 0.8498 (m-30) REVERT: I 203 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8368 (mm-40) outliers start: 8 outliers final: 4 residues processed: 212 average time/residue: 0.2782 time to fit residues: 90.5464 Evaluate side-chains 207 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 203 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain H residue 17 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 128 optimal weight: 0.5980 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.055064 restraints weight = 142043.695| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.49 r_work: 0.2665 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16839 Z= 0.173 Angle : 0.468 4.512 22734 Z= 0.268 Chirality : 0.042 0.143 2655 Planarity : 0.004 0.067 2898 Dihedral : 3.614 12.304 2250 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.81 % Allowed : 5.07 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.19), residues: 2061 helix: 3.31 (0.17), residues: 864 sheet: -0.09 (0.20), residues: 612 loop : 0.40 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 60 TYR 0.010 0.001 TYR F 229 PHE 0.009 0.001 PHE E 58 HIS 0.000 0.000 HIS E 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (16839) covalent geometry : angle 0.46845 / 0.27 (22734) hydrogen bonds : bond 0.04245 / 2.87 ( 1078) hydrogen bonds : angle 4.72087 / 3.32 ( 3612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.8801 (m-30) cc_final: 0.8581 (m-30) REVERT: A 203 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8324 (mm-40) REVERT: C 157 ASP cc_start: 0.8832 (m-30) cc_final: 0.8562 (m-30) REVERT: C 203 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8302 (mm-40) REVERT: E 203 GLN cc_start: 0.8731 (tp-100) cc_final: 0.8305 (mm-40) REVERT: E 222 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8370 (mmm-85) REVERT: F 157 ASP cc_start: 0.8900 (m-30) cc_final: 0.8461 (m-30) REVERT: F 203 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8344 (mm-40) REVERT: F 222 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.8298 (mmm-85) REVERT: G 203 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8478 (mm-40) REVERT: G 222 ARG cc_start: 0.8539 (mmm-85) cc_final: 0.8273 (ttm110) REVERT: H 157 ASP cc_start: 0.8850 (m-30) cc_final: 0.8464 (m-30) REVERT: I 157 ASP cc_start: 0.8963 (m-30) cc_final: 0.8556 (m-30) REVERT: I 203 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8323 (mm-40) outliers start: 15 outliers final: 10 residues processed: 207 average time/residue: 0.2638 time to fit residues: 84.0523 Evaluate side-chains 200 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain I residue 154 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 142 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.054796 restraints weight = 138378.377| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.42 r_work: 0.2710 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16839 Z= 0.144 Angle : 0.455 4.413 22734 Z= 0.257 Chirality : 0.042 0.140 2655 Planarity : 0.004 0.062 2898 Dihedral : 3.568 11.999 2250 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.97 % Allowed : 5.72 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.19), residues: 2061 helix: 3.33 (0.17), residues: 864 sheet: -0.12 (0.21), residues: 612 loop : 0.52 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 222 TYR 0.009 0.001 TYR B 229 PHE 0.008 0.001 PHE A 7 HIS 0.000 0.000 HIS G 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16839) covalent geometry : angle 0.45517 / 0.26 (22734) hydrogen bonds : bond 0.03945 / 2.65 ( 1078) hydrogen bonds : angle 4.48942 / 3.15 ( 3612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8384 (tp40) cc_final: 0.7939 (pm20) REVERT: A 157 ASP cc_start: 0.8832 (m-30) cc_final: 0.8599 (m-30) REVERT: A 203 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8309 (mm-40) REVERT: C 157 ASP cc_start: 0.8868 (m-30) cc_final: 0.8600 (m-30) REVERT: C 203 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8209 (mm-40) REVERT: D 203 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8167 (tm-30) REVERT: E 222 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8417 (mmm-85) REVERT: F 157 ASP cc_start: 0.8941 (m-30) cc_final: 0.8534 (m-30) REVERT: F 203 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8327 (mm-40) REVERT: F 222 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.8311 (ttm110) REVERT: H 113 GLN cc_start: 0.8380 (tp40) cc_final: 0.7853 (pm20) REVERT: H 157 ASP cc_start: 0.8857 (m-30) cc_final: 0.8468 (m-30) REVERT: H 203 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8129 (tm-30) REVERT: I 157 ASP cc_start: 0.8994 (m-30) cc_final: 0.8599 (m-30) REVERT: I 203 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8288 (mm-40) outliers start: 18 outliers final: 12 residues processed: 205 average time/residue: 0.2891 time to fit residues: 92.2403 Evaluate side-chains 197 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain I residue 154 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 140 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.065154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.052754 restraints weight = 140926.869| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.47 r_work: 0.2688 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 16839 Z= 0.229 Angle : 0.486 4.925 22734 Z= 0.276 Chirality : 0.043 0.135 2655 Planarity : 0.004 0.065 2898 Dihedral : 3.682 12.593 2250 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.08 % Allowed : 6.63 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.19), residues: 2061 helix: 3.11 (0.17), residues: 864 sheet: -0.38 (0.20), residues: 630 loop : 0.60 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 60 TYR 0.014 0.001 TYR I 156 PHE 0.010 0.001 PHE E 58 HIS 0.001 0.000 HIS I 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (16839) covalent geometry : angle 0.48586 / 0.28 (22734) hydrogen bonds : bond 0.04179 / 2.80 ( 1078) hydrogen bonds : angle 4.48810 / 3.15 ( 3612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.8841 (m-30) cc_final: 0.8602 (m-30) REVERT: A 203 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8305 (mm-40) REVERT: C 157 ASP cc_start: 0.8893 (m-30) cc_final: 0.8625 (m-30) REVERT: C 203 GLN cc_start: 0.8725 (tp-100) cc_final: 0.8254 (mm-40) REVERT: D 203 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8246 (tm-30) REVERT: E 203 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8404 (mm-40) REVERT: F 157 ASP cc_start: 0.8996 (m-30) cc_final: 0.8596 (m-30) REVERT: F 203 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8358 (mm-40) REVERT: F 222 ARG cc_start: 0.8623 (mtm-85) cc_final: 0.8400 (ttm110) REVERT: G 203 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8385 (mm-40) REVERT: G 222 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8333 (mmm-85) REVERT: H 157 ASP cc_start: 0.8901 (m-30) cc_final: 0.8502 (m-30) REVERT: H 203 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8097 (tm-30) REVERT: I 157 ASP cc_start: 0.8981 (m-30) cc_final: 0.8581 (m-30) REVERT: I 203 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8285 (mm-40) outliers start: 20 outliers final: 15 residues processed: 193 average time/residue: 0.2705 time to fit residues: 80.9319 Evaluate side-chains 201 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain I residue 154 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 192 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 187 optimal weight: 0.0050 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.055259 restraints weight = 138794.964| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.44 r_work: 0.2713 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16839 Z= 0.110 Angle : 0.450 5.271 22734 Z= 0.251 Chirality : 0.042 0.139 2655 Planarity : 0.004 0.062 2898 Dihedral : 3.565 11.443 2250 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.76 % Allowed : 7.17 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.20), residues: 2061 helix: 3.34 (0.17), residues: 864 sheet: -0.20 (0.21), residues: 612 loop : 0.66 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 222 TYR 0.008 0.001 TYR B 229 PHE 0.009 0.001 PHE H 58 HIS 0.001 0.000 HIS F 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (16839) covalent geometry : angle 0.44960 / 0.25 (22734) hydrogen bonds : bond 0.03709 / 2.47 ( 1078) hydrogen bonds : angle 4.20468 / 2.96 ( 3612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8312 (tp40) cc_final: 0.7797 (pm20) REVERT: A 157 ASP cc_start: 0.8816 (m-30) cc_final: 0.8569 (m-30) REVERT: A 203 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8302 (mm-40) REVERT: B 203 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8331 (tm-30) REVERT: C 157 ASP cc_start: 0.8926 (m-30) cc_final: 0.8661 (m-30) REVERT: C 203 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8216 (mm-40) REVERT: D 203 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8243 (tm-30) REVERT: E 203 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8285 (mm-40) REVERT: E 222 ARG cc_start: 0.8608 (mmm-85) cc_final: 0.8310 (mmm-85) REVERT: F 157 ASP cc_start: 0.8984 (m-30) cc_final: 0.8569 (m-30) REVERT: F 203 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8347 (mm-40) REVERT: H 157 ASP cc_start: 0.8877 (m-30) cc_final: 0.8474 (m-30) REVERT: H 203 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8084 (tm-30) REVERT: I 157 ASP cc_start: 0.9022 (m-30) cc_final: 0.8623 (m-30) REVERT: I 203 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8261 (mm-40) outliers start: 14 outliers final: 4 residues processed: 208 average time/residue: 0.2978 time to fit residues: 96.0586 Evaluate side-chains 194 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain H residue 17 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 21 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 151 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054822 restraints weight = 139761.696| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.45 r_work: 0.2712 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16839 Z= 0.134 Angle : 0.446 4.729 22734 Z= 0.250 Chirality : 0.042 0.135 2655 Planarity : 0.004 0.063 2898 Dihedral : 3.532 11.399 2250 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.81 % Allowed : 7.66 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.20), residues: 2061 helix: 3.34 (0.17), residues: 864 sheet: -0.33 (0.20), residues: 630 loop : 0.80 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 60 TYR 0.010 0.001 TYR E 156 PHE 0.008 0.001 PHE F 58 HIS 0.000 0.000 HIS F 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16839) covalent geometry : angle 0.44632 / 0.25 (22734) hydrogen bonds : bond 0.03668 / 2.44 ( 1078) hydrogen bonds : angle 4.16584 / 2.93 ( 3612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8391 (tp40) cc_final: 0.7905 (pm20) REVERT: A 203 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8310 (mm-40) REVERT: B 203 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8357 (tm-30) REVERT: C 157 ASP cc_start: 0.8909 (m-30) cc_final: 0.8643 (m-30) REVERT: C 203 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8247 (mm-40) REVERT: D 203 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8317 (tm-30) REVERT: E 203 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8311 (mm-40) REVERT: E 222 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8314 (mmm-85) REVERT: F 157 ASP cc_start: 0.8962 (m-30) cc_final: 0.8538 (m-30) REVERT: F 203 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8363 (mm-40) REVERT: H 113 GLN cc_start: 0.8387 (tp40) cc_final: 0.7813 (pm20) REVERT: H 157 ASP cc_start: 0.8881 (m-30) cc_final: 0.8472 (m-30) REVERT: H 203 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8084 (tm-30) REVERT: I 157 ASP cc_start: 0.9025 (m-30) cc_final: 0.8616 (m-30) REVERT: I 203 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8286 (mm-40) outliers start: 15 outliers final: 13 residues processed: 200 average time/residue: 0.2887 time to fit residues: 90.8097 Evaluate side-chains 199 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain I residue 154 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.067645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.055359 restraints weight = 140975.434| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.45 r_work: 0.2703 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16839 Z= 0.176 Angle : 0.470 5.790 22734 Z= 0.264 Chirality : 0.042 0.135 2655 Planarity : 0.004 0.063 2898 Dihedral : 3.554 11.723 2250 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.81 % Allowed : 7.98 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.20), residues: 2061 helix: 3.22 (0.17), residues: 864 sheet: -0.36 (0.20), residues: 630 loop : 0.81 (0.29), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 60 TYR 0.009 0.001 TYR B 229 PHE 0.009 0.001 PHE E 58 HIS 0.001 0.000 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (16839) covalent geometry : angle 0.46984 / 0.26 (22734) hydrogen bonds : bond 0.03783 / 2.53 ( 1078) hydrogen bonds : angle 4.21165 / 2.96 ( 3612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8432 (tp40) cc_final: 0.7930 (pm20) REVERT: A 203 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8303 (mm-40) REVERT: B 203 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8351 (tm-30) REVERT: C 157 ASP cc_start: 0.8925 (m-30) cc_final: 0.8654 (m-30) REVERT: C 203 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8243 (mm-40) REVERT: D 203 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8302 (tm-30) REVERT: E 203 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8327 (mm-40) REVERT: E 222 ARG cc_start: 0.8607 (mmm-85) cc_final: 0.8296 (mmm-85) REVERT: F 154 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: F 157 ASP cc_start: 0.8991 (m-30) cc_final: 0.8542 (m-30) REVERT: F 203 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8381 (mm-40) REVERT: H 157 ASP cc_start: 0.8863 (m-30) cc_final: 0.8450 (m-30) REVERT: H 203 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8136 (tm-30) REVERT: I 157 ASP cc_start: 0.9006 (m-30) cc_final: 0.8612 (m-30) REVERT: I 203 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8302 (mm-40) outliers start: 15 outliers final: 11 residues processed: 193 average time/residue: 0.2872 time to fit residues: 87.2082 Evaluate side-chains 195 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 154 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 167 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 171 GLN F 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.067854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.055763 restraints weight = 138280.459| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.34 r_work: 0.2718 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16839 Z= 0.108 Angle : 0.441 5.236 22734 Z= 0.245 Chirality : 0.042 0.138 2655 Planarity : 0.004 0.062 2898 Dihedral : 3.489 11.276 2250 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.43 % Allowed : 8.58 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.20), residues: 2061 helix: 3.38 (0.17), residues: 864 sheet: -0.35 (0.20), residues: 630 loop : 0.90 (0.29), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 35 TYR 0.008 0.001 TYR B 229 PHE 0.009 0.001 PHE H 58 HIS 0.000 0.000 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (16839) covalent geometry : angle 0.44110 / 0.24 (22734) hydrogen bonds : bond 0.03525 / 2.34 ( 1078) hydrogen bonds : angle 4.04228 / 2.84 ( 3612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8445 (tp40) cc_final: 0.7956 (pm20) REVERT: A 203 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8332 (mm-40) REVERT: B 203 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8408 (tm-30) REVERT: C 157 ASP cc_start: 0.8914 (m-30) cc_final: 0.8626 (m-30) REVERT: C 203 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8247 (mm-40) REVERT: D 203 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8344 (tm-30) REVERT: E 203 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8323 (mm-40) REVERT: E 222 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8222 (mmm-85) REVERT: F 157 ASP cc_start: 0.8961 (m-30) cc_final: 0.8518 (m-30) REVERT: F 203 GLN cc_start: 0.8656 (tp-100) cc_final: 0.8344 (mm-40) REVERT: G 203 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8215 (tm-30) REVERT: H 157 ASP cc_start: 0.8847 (m-30) cc_final: 0.8423 (m-30) REVERT: H 203 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8050 (tm-30) REVERT: I 157 ASP cc_start: 0.9022 (m-30) cc_final: 0.8605 (m-30) REVERT: I 203 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8290 (mm-40) outliers start: 8 outliers final: 6 residues processed: 197 average time/residue: 0.2866 time to fit residues: 88.7044 Evaluate side-chains 194 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 188 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 17 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 73 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN E 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.054888 restraints weight = 140556.040| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.43 r_work: 0.2704 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16839 Z= 0.189 Angle : 0.475 6.404 22734 Z= 0.267 Chirality : 0.042 0.134 2655 Planarity : 0.004 0.064 2898 Dihedral : 3.524 11.764 2250 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.43 % Allowed : 8.90 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.20), residues: 2061 helix: 3.23 (0.17), residues: 864 sheet: -0.35 (0.20), residues: 630 loop : 0.82 (0.29), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 60 TYR 0.009 0.001 TYR B 229 PHE 0.009 0.001 PHE E 58 HIS 0.001 0.000 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (16839) covalent geometry : angle 0.47472 / 0.27 (22734) hydrogen bonds : bond 0.03732 / 2.49 ( 1078) hydrogen bonds : angle 4.16188 / 2.92 ( 3612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8322 (mm-40) REVERT: B 203 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8390 (tm-30) REVERT: C 157 ASP cc_start: 0.8929 (m-30) cc_final: 0.8647 (m-30) REVERT: C 203 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8240 (mm-40) REVERT: D 203 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8359 (tm-30) REVERT: E 203 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8342 (mm-40) REVERT: F 157 ASP cc_start: 0.8998 (m-30) cc_final: 0.8556 (m-30) REVERT: F 203 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8369 (mm-40) REVERT: G 203 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8299 (tm-30) REVERT: G 222 ARG cc_start: 0.8581 (mmm-85) cc_final: 0.8326 (mmm-85) REVERT: H 157 ASP cc_start: 0.8854 (m-30) cc_final: 0.8415 (m-30) REVERT: H 203 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8124 (tm-30) REVERT: I 157 ASP cc_start: 0.9007 (m-30) cc_final: 0.8604 (m-30) REVERT: I 203 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8294 (mm-40) outliers start: 8 outliers final: 6 residues processed: 194 average time/residue: 0.2909 time to fit residues: 88.4385 Evaluate side-chains 188 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 17 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 125 optimal weight: 4.9990 chunk 104 optimal weight: 0.2980 chunk 148 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 171 GLN F 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056359 restraints weight = 140344.803| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.47 r_work: 0.2726 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16839 Z= 0.101 Angle : 0.443 5.393 22734 Z= 0.245 Chirality : 0.042 0.139 2655 Planarity : 0.004 0.061 2898 Dihedral : 3.472 11.273 2250 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.27 % Allowed : 9.01 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.20), residues: 2061 helix: 3.39 (0.17), residues: 864 sheet: -0.33 (0.20), residues: 630 loop : 0.92 (0.29), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 60 TYR 0.008 0.001 TYR B 229 PHE 0.009 0.001 PHE H 58 HIS 0.000 0.000 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (16839) covalent geometry : angle 0.44340 / 0.24 (22734) hydrogen bonds : bond 0.03474 / 2.30 ( 1078) hydrogen bonds : angle 4.00877 / 2.81 ( 3612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5526.27 seconds wall clock time: 94 minutes 58.49 seconds (5698.49 seconds total)