Starting phenix.real_space_refine on Wed Sep 25 09:37:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qew_13943/09_2024/7qew_13943.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qew_13943/09_2024/7qew_13943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qew_13943/09_2024/7qew_13943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qew_13943/09_2024/7qew_13943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qew_13943/09_2024/7qew_13943.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qew_13943/09_2024/7qew_13943.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 84 5.16 5 C 6384 2.51 5 N 1476 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9702 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1530 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 7.61, per 1000 atoms: 0.78 Number of scatterers: 9702 At special positions: 0 Unit cell: (96.9, 107.95, 89.25, 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 84 16.00 O 1758 8.00 N 1476 7.00 C 6384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 180 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 180 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 169 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 180 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 180 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 180 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 169 " distance=2.03 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: 2.35 Conformation dependent library (CDL) restraints added in 985.0 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 72.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'G' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 39 removed outlier: 3.606A pdb=" N PHE G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.834A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 39 through 44' Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 100 Proline residue: G 87 - end of helix removed outlier: 3.944A pdb=" N ALA G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE G 140 " --> pdb=" O TYR G 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE G 145 " --> pdb=" O PHE G 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR G 158 " --> pdb=" O PHE G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG G 216 " --> pdb=" O TYR G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.833A pdb=" N VAL H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 39 through 44' Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 100 Proline residue: H 87 - end of helix removed outlier: 3.944A pdb=" N ALA H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE H 140 " --> pdb=" O TYR H 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE H 141 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 158 " --> pdb=" O PHE H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 15 removed outlier: 4.091A pdb=" N LYS I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 44 removed outlier: 3.833A pdb=" N VAL I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 39 through 44' Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 100 Proline residue: I 87 - end of helix removed outlier: 3.944A pdb=" N ALA I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 159 removed outlier: 3.587A pdb=" N ILE I 140 " --> pdb=" O TYR I 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE I 141 " --> pdb=" O THR I 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL I 144 " --> pdb=" O ILE I 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE I 145 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR I 158 " --> pdb=" O PHE I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG I 216 " --> pdb=" O TYR I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 44 removed outlier: 3.834A pdb=" N VAL J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 39 through 44' Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 100 Proline residue: J 87 - end of helix removed outlier: 3.944A pdb=" N ALA J 96 " --> pdb=" O ALA J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE J 140 " --> pdb=" O TYR J 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE J 141 " --> pdb=" O THR J 137 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 144 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE J 145 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR J 158 " --> pdb=" O PHE J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG J 216 " --> pdb=" O TYR J 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 15 removed outlier: 4.091A pdb=" N LYS K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.833A pdb=" N VAL K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 100 Proline residue: K 87 - end of helix removed outlier: 3.944A pdb=" N ALA K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 159 removed outlier: 3.587A pdb=" N ILE K 140 " --> pdb=" O TYR K 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE K 141 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL K 144 " --> pdb=" O ILE K 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR K 158 " --> pdb=" O PHE K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG K 216 " --> pdb=" O TYR K 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 15 removed outlier: 4.092A pdb=" N LYS L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 39 removed outlier: 3.607A pdb=" N PHE L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 44 removed outlier: 3.834A pdb=" N VAL L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 39 through 44' Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 100 Proline residue: L 87 - end of helix removed outlier: 3.944A pdb=" N ALA L 96 " --> pdb=" O ALA L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 159 removed outlier: 3.586A pdb=" N ILE L 140 " --> pdb=" O TYR L 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE L 141 " --> pdb=" O THR L 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL L 144 " --> pdb=" O ILE L 140 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE L 145 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR L 158 " --> pdb=" O PHE L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 217 removed outlier: 3.696A pdb=" N ARG L 216 " --> pdb=" O TYR L 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'I' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'L' and resid 52 through 53 600 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2718 1.35 - 1.46: 2633 1.46 - 1.58: 4237 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 9708 Sorted by residual: bond pdb=" C1 LMT H 303 " pdb=" C2 LMT H 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C1 LMT L 303 " pdb=" C2 LMT L 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C1 LMT G 303 " pdb=" C2 LMT G 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C1 LMT J 305 " pdb=" C2 LMT J 305 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" C1 LMT J 303 " pdb=" C2 LMT J 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.05e+00 ... (remaining 9703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 12723 1.61 - 3.21: 153 3.21 - 4.82: 63 4.82 - 6.42: 99 6.42 - 8.03: 60 Bond angle restraints: 13098 Sorted by residual: angle pdb=" C6 LMT H 305 " pdb=" C7 LMT H 305 " pdb=" C8 LMT H 305 " ideal model delta sigma weight residual 117.26 109.23 8.03 3.00e+00 1.11e-01 7.17e+00 angle pdb=" C6 LMT I 305 " pdb=" C7 LMT I 305 " pdb=" C8 LMT I 305 " ideal model delta sigma weight residual 117.26 109.27 7.99 3.00e+00 1.11e-01 7.10e+00 angle pdb=" C6 LMT J 305 " pdb=" C7 LMT J 305 " pdb=" C8 LMT J 305 " ideal model delta sigma weight residual 117.26 109.28 7.98 3.00e+00 1.11e-01 7.08e+00 angle pdb=" C6 LMT K 305 " pdb=" C7 LMT K 305 " pdb=" C8 LMT K 305 " ideal model delta sigma weight residual 117.26 109.30 7.96 3.00e+00 1.11e-01 7.04e+00 angle pdb=" C6 LMT L 303 " pdb=" C7 LMT L 303 " pdb=" C8 LMT L 303 " ideal model delta sigma weight residual 117.26 109.31 7.95 3.00e+00 1.11e-01 7.03e+00 ... (remaining 13093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.92: 5056 11.92 - 23.85: 344 23.85 - 35.77: 144 35.77 - 47.70: 42 47.70 - 59.62: 30 Dihedral angle restraints: 5616 sinusoidal: 2298 harmonic: 3318 Sorted by residual: dihedral pdb=" CA ILE J 23 " pdb=" C ILE J 23 " pdb=" N TRP J 24 " pdb=" CA TRP J 24 " ideal model delta harmonic sigma weight residual -180.00 -165.41 -14.59 0 5.00e+00 4.00e-02 8.51e+00 dihedral pdb=" CA ILE I 23 " pdb=" C ILE I 23 " pdb=" N TRP I 24 " pdb=" CA TRP I 24 " ideal model delta harmonic sigma weight residual -180.00 -165.43 -14.57 0 5.00e+00 4.00e-02 8.49e+00 dihedral pdb=" CA ILE H 23 " pdb=" C ILE H 23 " pdb=" N TRP H 24 " pdb=" CA TRP H 24 " ideal model delta harmonic sigma weight residual -180.00 -165.45 -14.55 0 5.00e+00 4.00e-02 8.47e+00 ... (remaining 5613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 764 0.021 - 0.042: 395 0.042 - 0.063: 209 0.063 - 0.084: 51 0.084 - 0.105: 51 Chirality restraints: 1470 Sorted by residual: chirality pdb=" CA ILE H 71 " pdb=" N ILE H 71 " pdb=" C ILE H 71 " pdb=" CB ILE H 71 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.76e-01 chirality pdb=" CA PRO J 185 " pdb=" N PRO J 185 " pdb=" C PRO J 185 " pdb=" CB PRO J 185 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.70e-01 chirality pdb=" CA PRO H 185 " pdb=" N PRO H 185 " pdb=" C PRO H 185 " pdb=" CB PRO H 185 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.61e-01 ... (remaining 1467 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP I 172 " -0.016 5.00e-02 4.00e+02 2.49e-02 9.90e-01 pdb=" N PRO I 173 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO I 173 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 173 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP L 172 " 0.016 5.00e-02 4.00e+02 2.49e-02 9.89e-01 pdb=" N PRO L 173 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO L 173 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 173 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 172 " -0.016 5.00e-02 4.00e+02 2.49e-02 9.89e-01 pdb=" N PRO G 173 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " -0.012 5.00e-02 4.00e+02 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 455 2.73 - 3.27: 9822 3.27 - 3.82: 15831 3.82 - 4.36: 18958 4.36 - 4.90: 32012 Nonbonded interactions: 77078 Sorted by model distance: nonbonded pdb=" O ILE J 71 " pdb=" OH TYR J 158 " model vdw 2.191 3.040 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.191 3.040 nonbonded pdb=" O ILE L 71 " pdb=" OH TYR L 158 " model vdw 2.191 3.040 nonbonded pdb=" O ILE K 71 " pdb=" OH TYR K 158 " model vdw 2.192 3.040 nonbonded pdb=" O ILE G 71 " pdb=" OH TYR G 158 " model vdw 2.192 3.040 ... (remaining 77073 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 'G' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'H' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'I' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'J' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'K' and (resid 2 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'L' and (resid 2 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) } 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: 6.810 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 24.710 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 44.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 : 0.005 0.050 9708 Z= 0.288 Angle : 0.863 8.031 13098 Z= 0.353 Chirality : 0.035 0.105 1470 Planarity : 0.002 0.025 1542 Dihedral : 11.152 59.620 3414 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.18 % Allowed : 5.36 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1104 helix: 1.43 (0.18), residues: 714 sheet: 4.08 (0.68), residues: 66 loop : -1.08 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 24 HIS 0.001 0.000 HIS H 16 PHE 0.006 0.001 PHE I 51 TYR 0.004 0.001 TYR L 217 ARG 0.001 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 239 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 134 TRP cc_start: 0.8079 (m100) cc_final: 0.7759 (m100) REVERT: J 41 LYS cc_start: 0.8219 (tttt) cc_final: 0.7960 (tttp) REVERT: K 41 LYS cc_start: 0.8293 (tttt) cc_final: 0.8012 (tttp) outliers start: 22 outliers final: 1 residues processed: 250 average time/residue: 0.8992 time to fit residues: 245.3518 Evaluate side-chains 193 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9708 Z= 0.263 Angle : 0.669 8.606 13098 Z= 0.355 Chirality : 0.044 0.137 1470 Planarity : 0.004 0.024 1542 Dihedral : 9.194 59.856 1400 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.27 % Allowed : 12.30 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.29 (0.25), residues: 1104 helix: 2.35 (0.18), residues: 732 sheet: 3.21 (0.60), residues: 66 loop : -1.04 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 133 HIS 0.007 0.001 HIS G 73 PHE 0.015 0.002 PHE K 31 TYR 0.019 0.002 TYR J 65 ARG 0.009 0.001 ARG I 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 203 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 SER cc_start: 0.8578 (p) cc_final: 0.8315 (t) REVERT: K 41 LYS cc_start: 0.8435 (tttt) cc_final: 0.8164 (tttp) outliers start: 33 outliers final: 6 residues processed: 217 average time/residue: 0.9531 time to fit residues: 224.6797 Evaluate side-chains 198 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 192 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain I residue 41 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9708 Z= 0.331 Angle : 0.681 7.599 13098 Z= 0.359 Chirality : 0.046 0.151 1470 Planarity : 0.003 0.022 1542 Dihedral : 8.941 59.753 1398 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.77 % Allowed : 12.60 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.43 (0.25), residues: 1104 helix: 2.51 (0.18), residues: 738 sheet: 2.79 (0.55), residues: 66 loop : -1.09 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 133 HIS 0.007 0.001 HIS G 73 PHE 0.017 0.002 PHE L 51 TYR 0.015 0.002 TYR L 65 ARG 0.008 0.001 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7521 (tmm-80) REVERT: H 19 SER cc_start: 0.8532 (p) cc_final: 0.8325 (t) REVERT: H 23 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7669 (mp) REVERT: I 134 TRP cc_start: 0.6871 (OUTLIER) cc_final: 0.6644 (m-10) REVERT: K 41 LYS cc_start: 0.8454 (tttt) cc_final: 0.8211 (tttp) REVERT: K 209 GLU cc_start: 0.8465 (tp30) cc_final: 0.8256 (tp30) outliers start: 38 outliers final: 20 residues processed: 209 average time/residue: 0.9873 time to fit residues: 224.0871 Evaluate side-chains 204 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 134 TRP Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 199 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.5980 chunk 73 optimal weight: 0.0070 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9708 Z= 0.229 Angle : 0.624 8.347 13098 Z= 0.324 Chirality : 0.043 0.146 1470 Planarity : 0.003 0.032 1542 Dihedral : 8.381 59.888 1398 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.87 % Allowed : 13.10 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.69 (0.25), residues: 1104 helix: 2.77 (0.18), residues: 738 sheet: 2.73 (0.54), residues: 66 loop : -1.15 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 133 HIS 0.005 0.001 HIS J 73 PHE 0.020 0.002 PHE J 29 TYR 0.011 0.002 TYR L 65 ARG 0.009 0.001 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7609 (tmm-80) REVERT: H 23 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7702 (mp) REVERT: I 216 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7240 (tmm-80) REVERT: J 216 ARG cc_start: 0.7534 (ttp80) cc_final: 0.7274 (tmm-80) REVERT: K 41 LYS cc_start: 0.8469 (tttt) cc_final: 0.8266 (tttp) REVERT: K 216 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7353 (tmm-80) REVERT: L 216 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7688 (tmm-80) outliers start: 39 outliers final: 26 residues processed: 212 average time/residue: 1.0057 time to fit residues: 232.1439 Evaluate side-chains 211 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 16 HIS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9708 Z= 0.190 Angle : 0.604 8.255 13098 Z= 0.311 Chirality : 0.042 0.144 1470 Planarity : 0.003 0.025 1542 Dihedral : 7.979 58.871 1398 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.37 % Allowed : 14.48 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.88 (0.25), residues: 1104 helix: 2.97 (0.18), residues: 738 sheet: 2.70 (0.55), residues: 66 loop : -1.22 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 133 HIS 0.004 0.001 HIS G 73 PHE 0.014 0.001 PHE K 29 TYR 0.010 0.002 TYR K 68 ARG 0.006 0.001 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 216 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7639 (tmm-80) REVERT: H 23 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7695 (mp) REVERT: J 216 ARG cc_start: 0.7544 (ttp80) cc_final: 0.7299 (tmm-80) REVERT: K 41 LYS cc_start: 0.8388 (tttt) cc_final: 0.8184 (tttp) REVERT: K 216 ARG cc_start: 0.7627 (ttp80) cc_final: 0.7337 (tmm-80) REVERT: L 216 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7656 (tmm-80) outliers start: 34 outliers final: 21 residues processed: 206 average time/residue: 1.0200 time to fit residues: 227.5143 Evaluate side-chains 204 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 86 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9708 Z= 0.186 Angle : 0.611 8.966 13098 Z= 0.314 Chirality : 0.042 0.140 1470 Planarity : 0.003 0.020 1542 Dihedral : 7.681 59.609 1398 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.57 % Allowed : 15.18 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.98 (0.25), residues: 1104 helix: 3.08 (0.18), residues: 738 sheet: 2.67 (0.55), residues: 66 loop : -1.24 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 133 HIS 0.004 0.000 HIS G 73 PHE 0.013 0.001 PHE K 29 TYR 0.011 0.001 TYR H 68 ARG 0.005 0.001 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 193 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7599 (mttp) REVERT: H 23 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7764 (mp) REVERT: J 216 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7393 (tmm-80) REVERT: K 41 LYS cc_start: 0.8369 (tttt) cc_final: 0.8120 (tttp) REVERT: K 216 ARG cc_start: 0.7693 (ttp80) cc_final: 0.7440 (tmm-80) outliers start: 36 outliers final: 21 residues processed: 210 average time/residue: 1.0086 time to fit residues: 229.4151 Evaluate side-chains 206 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 16 HIS Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9708 Z= 0.314 Angle : 0.679 9.795 13098 Z= 0.356 Chirality : 0.045 0.156 1470 Planarity : 0.003 0.017 1542 Dihedral : 7.859 59.962 1398 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.37 % Allowed : 16.17 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.96 (0.25), residues: 1104 helix: 3.02 (0.18), residues: 738 sheet: 2.63 (0.55), residues: 66 loop : -1.13 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 134 HIS 0.004 0.001 HIS J 73 PHE 0.016 0.002 PHE L 51 TYR 0.017 0.002 TYR H 68 ARG 0.004 0.001 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 LYS cc_start: 0.7905 (mmtp) cc_final: 0.7660 (mttp) REVERT: H 216 ARG cc_start: 0.7561 (tmm-80) cc_final: 0.7350 (tmm-80) REVERT: K 41 LYS cc_start: 0.8403 (tttt) cc_final: 0.8202 (tttp) REVERT: K 216 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7354 (tmm-80) REVERT: L 22 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7488 (mttp) outliers start: 34 outliers final: 27 residues processed: 208 average time/residue: 1.0063 time to fit residues: 226.7518 Evaluate side-chains 210 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain L residue 22 LYS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 213 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9708 Z= 0.219 Angle : 0.665 10.847 13098 Z= 0.342 Chirality : 0.043 0.154 1470 Planarity : 0.003 0.018 1542 Dihedral : 7.588 59.442 1398 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.78 % Allowed : 17.16 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.02 (0.25), residues: 1104 helix: 3.11 (0.18), residues: 738 sheet: 2.63 (0.55), residues: 66 loop : -1.22 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 134 HIS 0.004 0.001 HIS J 73 PHE 0.022 0.002 PHE G 29 TYR 0.012 0.002 TYR H 68 ARG 0.005 0.000 ARG K 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 LYS cc_start: 0.7877 (mmtp) cc_final: 0.7648 (mttp) REVERT: H 216 ARG cc_start: 0.7583 (tmm-80) cc_final: 0.7362 (tmm-80) REVERT: K 41 LYS cc_start: 0.8380 (tttt) cc_final: 0.8165 (tttp) REVERT: K 216 ARG cc_start: 0.7737 (ttp80) cc_final: 0.7494 (tmm-80) outliers start: 28 outliers final: 21 residues processed: 206 average time/residue: 0.9965 time to fit residues: 222.0962 Evaluate side-chains 204 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 16 HIS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0980 chunk 97 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 91 optimal weight: 0.3980 chunk 96 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9708 Z= 0.162 Angle : 0.623 11.616 13098 Z= 0.320 Chirality : 0.041 0.159 1470 Planarity : 0.003 0.040 1542 Dihedral : 6.984 59.644 1398 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.28 % Allowed : 17.96 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.09 (0.25), residues: 1104 helix: 3.22 (0.17), residues: 738 sheet: 2.58 (0.55), residues: 66 loop : -1.34 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 134 HIS 0.003 0.000 HIS J 73 PHE 0.016 0.001 PHE J 29 TYR 0.008 0.001 TYR K 68 ARG 0.015 0.000 ARG J 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 41 LYS cc_start: 0.8339 (tttt) cc_final: 0.8099 (tttp) REVERT: K 216 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7419 (tmm-80) outliers start: 23 outliers final: 15 residues processed: 207 average time/residue: 1.0329 time to fit residues: 231.5187 Evaluate side-chains 200 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9708 Z= 0.215 Angle : 0.677 12.151 13098 Z= 0.346 Chirality : 0.043 0.163 1470 Planarity : 0.003 0.019 1542 Dihedral : 6.914 57.728 1398 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.69 % Allowed : 18.75 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.10 (0.25), residues: 1104 helix: 3.20 (0.18), residues: 738 sheet: 2.67 (0.56), residues: 66 loop : -1.28 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 134 HIS 0.003 0.000 HIS G 73 PHE 0.024 0.002 PHE L 29 TYR 0.012 0.002 TYR H 68 ARG 0.004 0.000 ARG K 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 41 LYS cc_start: 0.8350 (tttt) cc_final: 0.8134 (tttp) REVERT: K 41 LYS cc_start: 0.8327 (tttt) cc_final: 0.8085 (tttp) REVERT: K 216 ARG cc_start: 0.7732 (ttp80) cc_final: 0.7413 (tmm-80) outliers start: 17 outliers final: 16 residues processed: 206 average time/residue: 1.0279 time to fit residues: 229.4072 Evaluate side-chains 202 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 HIS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 16 HIS Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 16 HIS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.124745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.080770 restraints weight = 14617.798| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.78 r_work: 0.2897 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9708 Z= 0.207 Angle : 0.666 12.174 13098 Z= 0.343 Chirality : 0.042 0.161 1470 Planarity : 0.003 0.048 1542 Dihedral : 6.794 59.263 1398 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.49 % Allowed : 19.25 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.02 (0.25), residues: 1104 helix: 3.13 (0.17), residues: 738 sheet: 2.65 (0.56), residues: 66 loop : -1.30 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP H 134 HIS 0.004 0.001 HIS G 73 PHE 0.029 0.002 PHE G 29 TYR 0.011 0.001 TYR H 68 ARG 0.014 0.001 ARG J 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4538.43 seconds wall clock time: 79 minutes 47.77 seconds (4787.77 seconds total)