Starting phenix.real_space_refine on Fri Jun 13 01:50:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hx0_35070/06_2025/8hx0_35070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hx0_35070/06_2025/8hx0_35070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hx0_35070/06_2025/8hx0_35070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hx0_35070/06_2025/8hx0_35070.map" model { file = "/net/cci-nas-00/data/ceres_data/8hx0_35070/06_2025/8hx0_35070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hx0_35070/06_2025/8hx0_35070.cif" } resolution = 2.9 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= -0.001 sd= 0.125 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 12 5.16 5 C 9222 2.51 5 N 2715 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14919 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1250 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1229 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1250 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1229 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1250 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1229 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 9.71, per 1000 atoms: 0.65 Number of scatterers: 14919 At special positions: 0 Unit cell: (105.08, 105.82, 99.9, 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 12 16.00 O 2970 8.00 N 2715 7.00 C 9222 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: 3.59 Conformation dependent library (CDL) restraints added in 1.9 seconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3618 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 4 sheets defined 77.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 16 through 43 Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 84 through 92 Processing helix chain 'A' and resid 104 through 133 removed outlier: 4.226A pdb=" N ASP A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 156 removed outlier: 3.761A pdb=" N LEU A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 44 removed outlier: 3.578A pdb=" N ASP B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 77 removed outlier: 3.855A pdb=" N LEU B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 Processing helix chain 'B' and resid 103 through 131 removed outlier: 4.519A pdb=" N ASP B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 156 removed outlier: 3.578A pdb=" N LEU B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'C' and resid 16 through 43 removed outlier: 3.599A pdb=" N ASP C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 77 Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'C' and resid 104 through 133 removed outlier: 4.585A pdb=" N ASP C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALA C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 156 removed outlier: 3.673A pdb=" N LEU C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'D' and resid 16 through 44 removed outlier: 3.760A pdb=" N VAL D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 77 removed outlier: 4.025A pdb=" N LEU D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP D 57 " --> pdb=" O HIS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 92 Processing helix chain 'D' and resid 103 through 133 removed outlier: 4.302A pdb=" N ASP D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 156 removed outlier: 3.677A pdb=" N LEU D 139 " --> pdb=" O SER D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'E' and resid 16 through 44 Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 84 through 92 Processing helix chain 'E' and resid 103 through 133 removed outlier: 4.200A pdb=" N ASP E 127 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 156 removed outlier: 3.782A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 44 removed outlier: 3.551A pdb=" N ASP G 29 " --> pdb=" O LYS G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 77 removed outlier: 3.936A pdb=" N LEU G 52 " --> pdb=" O ASN G 48 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP G 57 " --> pdb=" O HIS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 92 Processing helix chain 'G' and resid 103 through 131 removed outlier: 4.483A pdb=" N ASP G 127 " --> pdb=" O ARG G 123 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA G 128 " --> pdb=" O ARG G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 156 removed outlier: 3.586A pdb=" N LEU G 139 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'I' and resid 16 through 43 removed outlier: 3.608A pdb=" N ASP I 29 " --> pdb=" O LYS I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 84 through 92 Processing helix chain 'I' and resid 104 through 133 removed outlier: 4.591A pdb=" N ASP I 127 " --> pdb=" O ARG I 123 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 156 removed outlier: 3.661A pdb=" N LEU I 139 " --> pdb=" O SER I 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 44 removed outlier: 3.688A pdb=" N VAL K 26 " --> pdb=" O ASN K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 77 removed outlier: 4.025A pdb=" N LEU K 52 " --> pdb=" O ASN K 48 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP K 57 " --> pdb=" O HIS K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 92 Processing helix chain 'K' and resid 103 through 133 removed outlier: 4.175A pdb=" N ASP K 127 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 156 removed outlier: 3.649A pdb=" N LEU K 139 " --> pdb=" O SER K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 159 No H-bonds generated for 'chain 'K' and resid 157 through 159' Processing helix chain 'F' and resid 16 through 44 Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 84 through 92 Processing helix chain 'F' and resid 103 through 133 removed outlier: 4.181A pdb=" N ASP F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 156 removed outlier: 3.814A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 44 removed outlier: 3.582A pdb=" N ASP H 29 " --> pdb=" O LYS H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 77 removed outlier: 3.835A pdb=" N LEU H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP H 57 " --> pdb=" O HIS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 92 Processing helix chain 'H' and resid 103 through 131 removed outlier: 4.565A pdb=" N ASP H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA H 128 " --> pdb=" O ARG H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 156 removed outlier: 3.575A pdb=" N LEU H 139 " --> pdb=" O SER H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 159 No H-bonds generated for 'chain 'H' and resid 157 through 159' Processing helix chain 'J' and resid 16 through 43 removed outlier: 3.604A pdb=" N ASP J 29 " --> pdb=" O LYS J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 77 Processing helix chain 'J' and resid 84 through 92 Processing helix chain 'J' and resid 104 through 133 removed outlier: 4.588A pdb=" N ASP J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ALA J 128 " --> pdb=" O ARG J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 156 removed outlier: 3.681A pdb=" N LEU J 139 " --> pdb=" O SER J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'L' and resid 16 through 44 removed outlier: 3.680A pdb=" N VAL L 26 " --> pdb=" O ASN L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 77 removed outlier: 4.037A pdb=" N LEU L 52 " --> pdb=" O ASN L 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP L 57 " --> pdb=" O HIS L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 92 Processing helix chain 'L' and resid 103 through 133 removed outlier: 4.196A pdb=" N ASP L 127 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA L 128 " --> pdb=" O ARG L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 156 removed outlier: 3.624A pdb=" N LEU L 139 " --> pdb=" O SER L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 159 No H-bonds generated for 'chain 'L' and resid 157 through 159' Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'C' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain 'I' and resid 44 through 45 Processing sheet with id=AA4, first strand: chain 'J' and resid 44 through 45 1169 hydrogen bonds defined for protein. 3507 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: 4.35 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5348 1.34 - 1.45: 1292 1.45 - 1.57: 8483 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 15147 Sorted by residual: bond pdb=" C VAL E 125 " pdb=" O VAL E 125 " ideal model delta sigma weight residual 1.237 1.252 -0.014 1.29e-02 6.01e+03 1.26e+00 bond pdb=" C VAL F 125 " pdb=" O VAL F 125 " ideal model delta sigma weight residual 1.237 1.251 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" C VAL A 125 " pdb=" O VAL A 125 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.35e-02 5.49e+03 1.13e+00 bond pdb=" SD MET H 74 " pdb=" CE MET H 74 " ideal model delta sigma weight residual 1.791 1.766 0.025 2.50e-02 1.60e+03 9.90e-01 bond pdb=" CB VAL D 125 " pdb=" CG2 VAL D 125 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.48e-01 ... (remaining 15142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 20155 1.61 - 3.23: 393 3.23 - 4.84: 43 4.84 - 6.46: 0 6.46 - 8.07: 1 Bond angle restraints: 20592 Sorted by residual: angle pdb=" N HIS G 126 " pdb=" CA HIS G 126 " pdb=" C HIS G 126 " ideal model delta sigma weight residual 111.07 115.72 -4.65 1.07e+00 8.73e-01 1.89e+01 angle pdb=" N HIS B 126 " pdb=" CA HIS B 126 " pdb=" C HIS B 126 " ideal model delta sigma weight residual 111.07 115.19 -4.12 1.07e+00 8.73e-01 1.48e+01 angle pdb=" N HIS H 126 " pdb=" CA HIS H 126 " pdb=" C HIS H 126 " ideal model delta sigma weight residual 111.07 114.32 -3.25 1.07e+00 8.73e-01 9.21e+00 angle pdb=" N HIS I 126 " pdb=" CA HIS I 126 " pdb=" C HIS I 126 " ideal model delta sigma weight residual 111.28 114.44 -3.16 1.09e+00 8.42e-01 8.39e+00 angle pdb=" N HIS C 126 " pdb=" CA HIS C 126 " pdb=" C HIS C 126 " ideal model delta sigma weight residual 111.28 114.32 -3.04 1.09e+00 8.42e-01 7.76e+00 ... (remaining 20587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 8473 17.33 - 34.66: 503 34.66 - 51.99: 102 51.99 - 69.32: 39 69.32 - 86.65: 27 Dihedral angle restraints: 9144 sinusoidal: 3612 harmonic: 5532 Sorted by residual: dihedral pdb=" CA PRO E 98 " pdb=" C PRO E 98 " pdb=" N ALA E 99 " pdb=" CA ALA E 99 " ideal model delta harmonic sigma weight residual -180.00 -161.89 -18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PRO F 98 " pdb=" C PRO F 98 " pdb=" N ALA F 99 " pdb=" CA ALA F 99 " ideal model delta harmonic sigma weight residual 180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA TRP F 42 " pdb=" C TRP F 42 " pdb=" N ASN F 43 " pdb=" CA ASN F 43 " ideal model delta harmonic sigma weight residual 180.00 -163.08 -16.92 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 9141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1390 0.026 - 0.051: 625 0.051 - 0.077: 292 0.077 - 0.103: 79 0.103 - 0.129: 29 Chirality restraints: 2415 Sorted by residual: chirality pdb=" CA ASP F 145 " pdb=" N ASP F 145 " pdb=" C ASP F 145 " pdb=" CB ASP F 145 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ASP E 145 " pdb=" N ASP E 145 " pdb=" C ASP E 145 " pdb=" CB ASP E 145 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CB VAL G 45 " pdb=" CA VAL G 45 " pdb=" CG1 VAL G 45 " pdb=" CG2 VAL G 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 2412 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE J 97 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO J 98 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO J 98 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO J 98 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 97 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO I 98 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO I 98 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 98 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 97 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO C 98 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 98 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 98 " -0.019 5.00e-02 4.00e+02 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2403 2.77 - 3.30: 15393 3.30 - 3.83: 25703 3.83 - 4.37: 29101 4.37 - 4.90: 52650 Nonbonded interactions: 125250 Sorted by model distance: nonbonded pdb=" OE1 GLN K 39 " pdb=" ND2 ASN K 43 " model vdw 2.234 3.120 nonbonded pdb=" O THR C 87 " pdb=" OG1 THR C 91 " model vdw 2.258 3.040 nonbonded pdb=" OE1 GLN D 39 " pdb=" ND2 ASN D 43 " model vdw 2.260 3.120 nonbonded pdb=" OE1 GLN L 39 " pdb=" ND2 ASN L 43 " model vdw 2.274 3.120 nonbonded pdb=" OE1 GLN I 39 " pdb=" ND2 ASN I 43 " model vdw 2.287 3.120 ... (remaining 125245 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' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or n \ ame CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C o \ r name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or na \ me CA or name C or name O or name CB )) or resid 161)) selection = (chain 'B' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'C' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'D' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 161)) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or n \ ame CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C o \ r name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or na \ me CA or name C or name O or name CB )) or resid 161)) selection = (chain 'F' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or n \ ame CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C o \ r name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or na \ me CA or name C or name O or name CB )) or resid 161)) selection = (chain 'G' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'H' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'I' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'J' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'K' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 161)) selection = (chain 'L' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 161)) } 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.520 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 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:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 0.032 15147 Z= 0.163 Angle : 0.545 8.075 20592 Z= 0.335 Chirality : 0.036 0.129 2415 Planarity : 0.004 0.039 2754 Dihedral : 13.324 86.651 5526 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.06 % Allowed : 0.00 % Favored : 99.94 % 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: 3.64 (0.19), residues: 1902 helix: 3.09 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.17 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 42 HIS 0.008 0.002 HIS J 53 PHE 0.011 0.002 PHE H 19 ARG 0.008 0.000 ARG I 155 Details of bonding type rmsd hydrogen bonds : bond 0.09258 ( 1169) hydrogen bonds : angle 3.63885 ( 3507) covalent geometry : bond 0.00322 (15147) covalent geometry : angle 0.54504 (20592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 2.360 Fit side-chains outliers start: 1 outliers final: 2 residues processed: 103 average time/residue: 2.3147 time to fit residues: 256.0514 Evaluate side-chains 84 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain L residue 29 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN C 150 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN G 150 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 GLN I 150 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 HIS ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 150 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN J 150 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 HIS ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 150 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103889 restraints weight = 15738.511| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.64 r_work: 0.3135 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15147 Z= 0.234 Angle : 0.561 5.524 20592 Z= 0.318 Chirality : 0.041 0.163 2415 Planarity : 0.004 0.036 2754 Dihedral : 4.714 56.284 2086 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.31 % Allowed : 3.96 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.16 (0.19), residues: 1902 helix: 2.72 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.09 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP L 152 HIS 0.014 0.002 HIS J 53 PHE 0.015 0.003 PHE D 19 ARG 0.003 0.001 ARG H 159 Details of bonding type rmsd hydrogen bonds : bond 0.09463 ( 1169) hydrogen bonds : angle 3.74895 ( 3507) covalent geometry : bond 0.00560 (15147) covalent geometry : angle 0.56117 (20592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 1.902 Fit side-chains REVERT: E 82 ASP cc_start: 0.8938 (t70) cc_final: 0.8718 (t70) REVERT: E 101 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7650 (mt-10) REVERT: E 127 ASP cc_start: 0.6761 (m-30) cc_final: 0.6549 (t70) REVERT: F 86 ASP cc_start: 0.7079 (m-30) cc_final: 0.6517 (m-30) outliers start: 5 outliers final: 1 residues processed: 125 average time/residue: 2.0085 time to fit residues: 272.5602 Evaluate side-chains 107 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 189 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN D 150 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111771 restraints weight = 15332.830| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.66 r_work: 0.3112 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15147 Z= 0.142 Angle : 0.452 5.865 20592 Z= 0.257 Chirality : 0.035 0.152 2415 Planarity : 0.004 0.034 2754 Dihedral : 4.372 55.524 2084 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.69 % Allowed : 5.28 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.19), residues: 1902 helix: 3.04 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.13 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 42 HIS 0.011 0.002 HIS J 53 PHE 0.012 0.002 PHE H 49 ARG 0.001 0.000 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.06966 ( 1169) hydrogen bonds : angle 3.49420 ( 3507) covalent geometry : bond 0.00281 (15147) covalent geometry : angle 0.45213 (20592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.542 Fit side-chains REVERT: E 82 ASP cc_start: 0.8880 (t0) cc_final: 0.8630 (t70) REVERT: J 148 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7511 (mt-10) outliers start: 11 outliers final: 6 residues processed: 101 average time/residue: 2.0287 time to fit residues: 220.8464 Evaluate side-chains 94 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.101998 restraints weight = 15782.202| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.65 r_work: 0.3030 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 15147 Z= 0.248 Angle : 0.569 6.030 20592 Z= 0.318 Chirality : 0.041 0.168 2415 Planarity : 0.004 0.037 2754 Dihedral : 4.785 56.217 2082 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.82 % Allowed : 6.23 % Favored : 92.96 % 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: 2.89 (0.19), residues: 1902 helix: 2.53 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.05 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 152 HIS 0.013 0.002 HIS J 53 PHE 0.015 0.003 PHE D 19 ARG 0.003 0.000 ARG J 73 Details of bonding type rmsd hydrogen bonds : bond 0.09779 ( 1169) hydrogen bonds : angle 3.75247 ( 3507) covalent geometry : bond 0.00603 (15147) covalent geometry : angle 0.56894 (20592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.496 Fit side-chains REVERT: A 127 ASP cc_start: 0.6818 (m-30) cc_final: 0.6572 (t70) REVERT: C 157 GLU cc_start: 0.7554 (tp30) cc_final: 0.7222 (tp30) REVERT: D 78 ASP cc_start: 0.7403 (t0) cc_final: 0.6878 (t0) REVERT: D 127 ASP cc_start: 0.6972 (m-30) cc_final: 0.6649 (t70) REVERT: E 127 ASP cc_start: 0.6736 (m-30) cc_final: 0.6524 (t70) REVERT: F 86 ASP cc_start: 0.7118 (m-30) cc_final: 0.6592 (m-30) REVERT: F 101 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7473 (mt-10) REVERT: H 82 ASP cc_start: 0.8811 (t0) cc_final: 0.8420 (t0) REVERT: H 86 ASP cc_start: 0.6900 (m-30) cc_final: 0.6648 (m-30) REVERT: J 148 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7633 (mt-10) outliers start: 13 outliers final: 10 residues processed: 141 average time/residue: 2.0502 time to fit residues: 314.8827 Evaluate side-chains 140 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 29 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106953 restraints weight = 15708.084| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.65 r_work: 0.3158 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15147 Z= 0.160 Angle : 0.469 6.150 20592 Z= 0.266 Chirality : 0.036 0.153 2415 Planarity : 0.004 0.035 2754 Dihedral : 4.485 55.442 2082 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.38 % Allowed : 6.79 % Favored : 91.82 % 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: 3.29 (0.19), residues: 1902 helix: 2.83 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.04 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 42 HIS 0.010 0.002 HIS J 53 PHE 0.014 0.002 PHE H 49 ARG 0.001 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.07609 ( 1169) hydrogen bonds : angle 3.55163 ( 3507) covalent geometry : bond 0.00340 (15147) covalent geometry : angle 0.46883 (20592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.706 Fit side-chains REVERT: A 45 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7407 (m) REVERT: A 148 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7592 (mt-10) REVERT: C 157 GLU cc_start: 0.7512 (tp30) cc_final: 0.7186 (tp30) REVERT: F 86 ASP cc_start: 0.7015 (m-30) cc_final: 0.6499 (m-30) REVERT: J 148 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7492 (mt-10) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 1.7828 time to fit residues: 214.1282 Evaluate side-chains 102 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 29 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 21 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 118 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111606 restraints weight = 15495.664| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.61 r_work: 0.3199 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15147 Z= 0.141 Angle : 0.442 5.772 20592 Z= 0.250 Chirality : 0.035 0.150 2415 Planarity : 0.003 0.034 2754 Dihedral : 4.349 55.643 2082 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.07 % Allowed : 7.74 % Favored : 91.19 % 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: 3.54 (0.19), residues: 1902 helix: 3.02 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.12 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 42 HIS 0.010 0.002 HIS J 53 PHE 0.013 0.002 PHE H 49 ARG 0.001 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.06857 ( 1169) hydrogen bonds : angle 3.43542 ( 3507) covalent geometry : bond 0.00286 (15147) covalent geometry : angle 0.44226 (20592) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.731 Fit side-chains REVERT: A 45 VAL cc_start: 0.7597 (OUTLIER) cc_final: 0.7316 (m) REVERT: A 127 ASP cc_start: 0.7081 (m-30) cc_final: 0.6876 (t0) REVERT: A 148 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7573 (mt-10) REVERT: C 157 GLU cc_start: 0.7515 (tp30) cc_final: 0.7187 (tp30) REVERT: H 157 GLU cc_start: 0.7599 (tp30) cc_final: 0.7259 (tp30) REVERT: J 148 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7429 (mt-10) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 2.0464 time to fit residues: 190.0840 Evaluate side-chains 86 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 95 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103973 restraints weight = 15825.856| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.66 r_work: 0.3118 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 15147 Z= 0.202 Angle : 0.511 5.836 20592 Z= 0.286 Chirality : 0.038 0.160 2415 Planarity : 0.004 0.036 2754 Dihedral : 4.642 55.732 2082 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.38 % Allowed : 7.80 % Favored : 90.82 % 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: 3.12 (0.19), residues: 1902 helix: 2.70 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.04 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 152 HIS 0.011 0.002 HIS J 53 PHE 0.012 0.002 PHE L 19 ARG 0.002 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.08711 ( 1169) hydrogen bonds : angle 3.61480 ( 3507) covalent geometry : bond 0.00473 (15147) covalent geometry : angle 0.51122 (20592) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.497 Fit side-chains REVERT: A 45 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.7426 (m) REVERT: A 127 ASP cc_start: 0.7156 (m-30) cc_final: 0.6935 (t0) REVERT: A 148 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7582 (mt-10) REVERT: C 157 GLU cc_start: 0.7546 (tp30) cc_final: 0.7190 (tp30) REVERT: F 101 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7448 (mt-10) REVERT: H 157 GLU cc_start: 0.7642 (tp30) cc_final: 0.7323 (tp30) REVERT: J 148 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7484 (mt-10) outliers start: 22 outliers final: 15 residues processed: 116 average time/residue: 1.5456 time to fit residues: 195.2952 Evaluate side-chains 112 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 176 optimal weight: 20.0000 chunk 188 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107554 restraints weight = 15551.848| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.62 r_work: 0.3143 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 15147 Z= 0.175 Angle : 0.483 5.883 20592 Z= 0.272 Chirality : 0.037 0.163 2415 Planarity : 0.004 0.034 2754 Dihedral : 4.559 55.532 2082 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.38 % Allowed : 8.18 % Favored : 90.44 % 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: 3.24 (0.19), residues: 1902 helix: 2.79 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.07 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 152 HIS 0.010 0.002 HIS J 53 PHE 0.013 0.002 PHE H 49 ARG 0.002 0.000 ARG L 73 Details of bonding type rmsd hydrogen bonds : bond 0.08029 ( 1169) hydrogen bonds : angle 3.56415 ( 3507) covalent geometry : bond 0.00390 (15147) covalent geometry : angle 0.48253 (20592) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.697 Fit side-chains REVERT: A 45 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7415 (m) REVERT: A 127 ASP cc_start: 0.7104 (m-30) cc_final: 0.6886 (t0) REVERT: A 148 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7601 (mt-10) REVERT: B 148 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7595 (mt-10) REVERT: C 157 GLU cc_start: 0.7541 (tp30) cc_final: 0.7221 (tp30) REVERT: F 86 ASP cc_start: 0.7028 (m-30) cc_final: 0.6506 (m-30) REVERT: F 101 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7350 (mt-10) REVERT: F 127 ASP cc_start: 0.7072 (m-30) cc_final: 0.6856 (t70) REVERT: H 157 GLU cc_start: 0.7671 (tp30) cc_final: 0.7292 (tp30) REVERT: J 148 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7474 (mt-10) outliers start: 22 outliers final: 16 residues processed: 112 average time/residue: 1.7029 time to fit residues: 206.7956 Evaluate side-chains 112 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4377 > 50: distance: 47 - 77: 18.505 distance: 56 - 91: 14.217 distance: 64 - 67: 3.069 distance: 65 - 99: 37.781 distance: 68 - 69: 10.161 distance: 68 - 71: 8.787 distance: 69 - 70: 22.420 distance: 69 - 77: 27.794 distance: 72 - 73: 8.388 distance: 74 - 76: 4.043 distance: 75 - 76: 5.205 distance: 77 - 78: 17.528 distance: 78 - 79: 18.125 distance: 78 - 81: 16.172 distance: 79 - 80: 5.432 distance: 79 - 91: 40.308 distance: 81 - 82: 11.959 distance: 82 - 83: 4.333 distance: 82 - 84: 4.028 distance: 83 - 85: 4.468 distance: 84 - 86: 4.803 distance: 84 - 87: 5.540 distance: 85 - 86: 4.502 distance: 87 - 89: 3.026 distance: 88 - 90: 5.787 distance: 89 - 90: 4.264 distance: 91 - 92: 23.190 distance: 92 - 93: 20.177 distance: 92 - 95: 29.829 distance: 93 - 94: 18.828 distance: 93 - 99: 60.326 distance: 95 - 96: 14.473 distance: 96 - 97: 26.588 distance: 96 - 98: 18.880 distance: 99 - 100: 26.814 distance: 100 - 101: 33.862 distance: 100 - 103: 6.097 distance: 101 - 102: 9.037 distance: 101 - 106: 57.478 distance: 103 - 104: 35.823 distance: 103 - 105: 45.245 distance: 106 - 107: 30.005 distance: 107 - 108: 10.656 distance: 107 - 110: 9.055 distance: 108 - 109: 38.051 distance: 108 - 113: 40.246 distance: 110 - 112: 8.817 distance: 113 - 114: 40.497 distance: 117 - 118: 26.177 distance: 118 - 119: 3.045 distance: 118 - 121: 24.255 distance: 119 - 120: 21.780 distance: 119 - 123: 48.769 distance: 121 - 122: 54.016 distance: 124 - 125: 42.370 distance: 124 - 127: 15.140 distance: 125 - 126: 17.929 distance: 125 - 131: 27.668 distance: 127 - 128: 26.120 distance: 128 - 129: 40.108 distance: 128 - 130: 24.134 distance: 131 - 132: 20.081 distance: 132 - 133: 17.020 distance: 132 - 135: 30.230 distance: 133 - 134: 40.917 distance: 133 - 142: 31.431 distance: 134 - 168: 29.649 distance: 135 - 136: 17.453 distance: 136 - 137: 25.960 distance: 136 - 138: 7.974 distance: 137 - 139: 20.564 distance: 138 - 140: 3.630 distance: 139 - 141: 7.995 distance: 140 - 141: 39.175 distance: 142 - 143: 20.676 distance: 143 - 144: 11.097 distance: 143 - 146: 46.351 distance: 144 - 145: 12.650 distance: 144 - 153: 24.004 distance: 145 - 178: 31.325 distance: 146 - 147: 31.263 distance: 147 - 148: 12.967 distance: 149 - 150: 8.611 distance: 150 - 151: 14.595 distance: 150 - 152: 36.719