Starting phenix.real_space_refine on Tue Dec 31 02:05:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hx0_35070/12_2024/8hx0_35070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hx0_35070/12_2024/8hx0_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_35070/12_2024/8hx0_35070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hx0_35070/12_2024/8hx0_35070.map" model { file = "/net/cci-nas-00/data/ceres_data/8hx0_35070/12_2024/8hx0_35070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hx0_35070/12_2024/8hx0_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-5532/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: 10.13, per 1000 atoms: 0.68 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: 3.90 Conformation dependent library (CDL) restraints added in 2.0 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: 4.52 Time building geometry restraints manager: 4.48 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: 0.00 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: 2.780 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: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 35.750 Find NCS groups from input model: 0.820 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.640 ------------------------------------------------------------------------------- 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= 0.212 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 *********************** 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 : 1.551 Fit side-chains outliers start: 1 outliers final: 2 residues processed: 103 average time/residue: 2.1561 time to fit residues: 238.3047 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 : 2.021 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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= 0.369 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 *********************** 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 : 1.699 Fit side-chains REVERT: F 86 ASP cc_start: 0.7323 (m-30) cc_final: 0.7108 (m-30) REVERT: J 148 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8167 (mt-10) outliers start: 5 outliers final: 1 residues processed: 125 average time/residue: 1.6010 time to fit residues: 218.2907 Evaluate side-chains 106 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 96 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0963 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= 0.209 Angle : 0.467 5.800 20592 Z= 0.266 Chirality : 0.036 0.154 2415 Planarity : 0.004 0.034 2754 Dihedral : 4.446 55.660 2084 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.82 % Allowed : 5.09 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.19), residues: 1902 helix: 2.95 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.11 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 42 HIS 0.012 0.002 HIS J 53 PHE 0.012 0.002 PHE H 49 ARG 0.002 0.000 ARG D 114 *********************** 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 107 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 1.645 Fit side-chains REVERT: A 148 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8177 (mt-10) REVERT: B 148 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8055 (mt-10) REVERT: E 148 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8049 (mt-10) REVERT: F 86 ASP cc_start: 0.7241 (m-30) cc_final: 0.7040 (m-30) outliers start: 13 outliers final: 7 residues processed: 102 average time/residue: 1.8252 time to fit residues: 201.3507 Evaluate side-chains 94 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 I residue 29 ASP Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain J residue 127 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1049 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= 0.175 Angle : 0.435 5.627 20592 Z= 0.246 Chirality : 0.035 0.151 2415 Planarity : 0.003 0.033 2754 Dihedral : 4.261 55.463 2082 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.82 % Allowed : 6.16 % Favored : 93.02 % 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: 3.69 (0.19), residues: 1902 helix: 3.12 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.19 (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 0.002 0.000 ARG D 114 *********************** 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 90 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.601 Fit side-chains REVERT: A 148 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8138 (mt-10) REVERT: E 148 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8045 (mt-10) REVERT: K 148 GLU cc_start: 0.8221 (mt-10) cc_final: 0.8004 (mt-10) REVERT: J 148 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8097 (mt-10) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 2.0621 time to fit residues: 192.8357 Evaluate side-chains 83 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 I residue 29 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 29 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1277 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= 0.327 Angle : 0.523 5.789 20592 Z= 0.293 Chirality : 0.039 0.162 2415 Planarity : 0.004 0.036 2754 Dihedral : 4.644 55.745 2082 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.13 % Allowed : 6.92 % Favored : 91.95 % 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: 3.15 (0.19), residues: 1902 helix: 2.71 (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 0.012 0.002 HIS J 53 PHE 0.013 0.002 PHE L 19 ARG 0.002 0.000 ARG F 102 *********************** 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 123 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.428 Fit side-chains REVERT: A 148 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8149 (mt-10) REVERT: B 148 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8095 (mt-10) REVERT: E 148 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8069 (mt-10) REVERT: H 150 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8344 (mm-40) REVERT: H 157 GLU cc_start: 0.7937 (tp30) cc_final: 0.7646 (tp30) REVERT: J 148 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8145 (mt-10) outliers start: 18 outliers final: 6 residues processed: 119 average time/residue: 1.6890 time to fit residues: 218.2553 Evaluate side-chains 107 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 29 ASP Chi-restraints excluded: chain H residue 150 GLN Chi-restraints excluded: chain J residue 127 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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** ** 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** F 41 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 15147 Z= 0.347 Angle : 0.536 6.289 20592 Z= 0.300 Chirality : 0.039 0.163 2415 Planarity : 0.004 0.036 2754 Dihedral : 4.759 55.269 2082 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.13 % Allowed : 7.74 % Favored : 91.13 % 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: 2.95 (0.19), residues: 1902 helix: 2.56 (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 0.006 0.002 TRP J 152 HIS 0.011 0.002 HIS J 53 PHE 0.014 0.002 PHE L 19 ARG 0.002 0.000 ARG L 73 *********************** 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 131 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.731 Fit side-chains REVERT: B 148 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8072 (mt-10) REVERT: E 148 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8100 (mt-10) REVERT: F 86 ASP cc_start: 0.7325 (m-30) cc_final: 0.7108 (m-30) REVERT: H 150 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8339 (mm-40) REVERT: H 157 GLU cc_start: 0.7978 (tp30) cc_final: 0.7704 (tp30) REVERT: J 148 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8144 (mt-10) outliers start: 18 outliers final: 12 residues processed: 126 average time/residue: 1.6064 time to fit residues: 220.2673 Evaluate side-chains 118 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B 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 E residue 45 VAL Chi-restraints excluded: chain E residue 125 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 150 GLN Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 29 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 185 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- 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** F 41 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1297 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= 0.180 Angle : 0.441 5.862 20592 Z= 0.250 Chirality : 0.035 0.151 2415 Planarity : 0.003 0.033 2754 Dihedral : 4.386 54.767 2082 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.57 % Allowed : 7.74 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.19), residues: 1902 helix: 3.02 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.18 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 42 HIS 0.010 0.002 HIS J 53 PHE 0.013 0.002 PHE K 49 ARG 0.001 0.000 ARG D 114 *********************** 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 101 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 1.627 Fit side-chains REVERT: A 148 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8150 (mt-10) REVERT: E 148 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8048 (mt-10) REVERT: H 157 GLU cc_start: 0.7866 (tp30) cc_final: 0.7607 (tp30) outliers start: 25 outliers final: 11 residues processed: 98 average time/residue: 1.9329 time to fit residues: 204.8319 Evaluate side-chains 85 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B 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 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 J residue 29 ASP Chi-restraints excluded: chain L residue 127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1292 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= 0.203 Angle : 0.451 5.504 20592 Z= 0.254 Chirality : 0.035 0.154 2415 Planarity : 0.004 0.034 2754 Dihedral : 4.396 54.809 2082 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.26 % Allowed : 8.11 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.19), residues: 1902 helix: 3.01 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.21 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 42 HIS 0.009 0.002 HIS J 53 PHE 0.012 0.002 PHE K 49 ARG 0.001 0.000 ARG F 102 *********************** 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 96 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.747 Fit side-chains REVERT: A 148 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 148 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8052 (mt-10) REVERT: E 148 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8052 (mt-10) REVERT: K 148 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8005 (mt-10) REVERT: H 157 GLU cc_start: 0.7847 (tp30) cc_final: 0.7586 (tp30) REVERT: J 148 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8108 (mt-10) outliers start: 20 outliers final: 14 residues processed: 93 average time/residue: 1.8703 time to fit residues: 187.8397 Evaluate side-chains 90 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP 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 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 127 ASP 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 127 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15147 Z= 0.283 Angle : 0.494 5.732 20592 Z= 0.277 Chirality : 0.037 0.159 2415 Planarity : 0.004 0.035 2754 Dihedral : 4.575 54.780 2082 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.32 % Allowed : 8.36 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.19), residues: 1902 helix: 2.80 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.16 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 152 HIS 0.010 0.002 HIS J 53 PHE 0.012 0.002 PHE K 49 ARG 0.002 0.000 ARG I 114 *********************** REFINEMENT MACRO_CYCLE 9 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 122 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.666 Fit side-chains REVERT: A 148 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8173 (mt-10) REVERT: B 148 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8078 (mt-10) REVERT: E 148 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8070 (mt-10) REVERT: K 148 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8025 (mt-10) REVERT: H 157 GLU cc_start: 0.7903 (tp30) cc_final: 0.7626 (tp30) REVERT: J 148 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8137 (mt-10) outliers start: 21 outliers final: 14 residues processed: 115 average time/residue: 1.8480 time to fit residues: 229.7531 Evaluate side-chains 113 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 29 ASP Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 152 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15147 Z= 0.169 Angle : 0.440 5.723 20592 Z= 0.249 Chirality : 0.035 0.152 2415 Planarity : 0.003 0.033 2754 Dihedral : 4.349 54.378 2082 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.13 % Allowed : 8.55 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.19), residues: 1902 helix: 3.08 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.22 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 42 HIS 0.009 0.002 HIS J 53 PHE 0.012 0.002 PHE K 49 ARG 0.001 0.000 ARG F 102 ********************** REFINEMENT MACRO_CYCLE 10 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: 18 poor density : 73 time to evaluate : 1.756 Fit side-chains REVERT: A 148 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 148 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8053 (mt-10) REVERT: E 148 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8035 (mt-10) REVERT: K 148 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7989 (mt-10) REVERT: H 157 GLU cc_start: 0.7863 (tp30) cc_final: 0.7613 (tp30) REVERT: J 148 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8103 (mt-10) outliers start: 18 outliers final: 15 residues processed: 88 average time/residue: 2.0789 time to fit residues: 198.8421 Evaluate side-chains 86 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 127 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 127 ASP Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.122134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102672 restraints weight = 15805.126| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.21 r_work: 0.3006 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 15147 Z= 0.329 Angle : 0.523 5.843 20592 Z= 0.292 Chirality : 0.039 0.162 2415 Planarity : 0.004 0.036 2754 Dihedral : 4.683 54.864 2082 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.13 % Allowed : 8.55 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.19), residues: 1902 helix: 2.68 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.15 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP G 42 HIS 0.011 0.002 HIS J 53 PHE 0.013 0.002 PHE L 19 ARG 0.002 0.000 ARG E 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4007.69 seconds wall clock time: 73 minutes 29.41 seconds (4409.41 seconds total)