Starting phenix.real_space_refine on Mon Nov 18 23:33:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k37_36846/11_2024/8k37_36846.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k37_36846/11_2024/8k37_36846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k37_36846/11_2024/8k37_36846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k37_36846/11_2024/8k37_36846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k37_36846/11_2024/8k37_36846.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k37_36846/11_2024/8k37_36846.cif" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= -0.006 sd= 1.080 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 60 5.16 5 C 11598 2.51 5 N 3138 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18528 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "H" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "I" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "J" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "K" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "L" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "A" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "B" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "C" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "D" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "E" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "F" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "M" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "N" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "O" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "P" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "Q" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "R" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Time building chain proxies: 11.30, per 1000 atoms: 0.61 Number of scatterers: 18528 At special positions: 0 Unit cell: (110.16, 107.44, 137.36, 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 60 16.00 O 3732 8.00 N 3138 7.00 C 11598 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: 4.46 Conformation dependent library (CDL) restraints added in 2.4 seconds 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 34 sheets defined 18.8% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'G' and resid 90 through 102 removed outlier: 3.557A pdb=" N GLN G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 155 removed outlier: 3.768A pdb=" N ASP G 154 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG G 155 " --> pdb=" O ALA G 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 151 through 155' Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 151 through 155 removed outlier: 3.647A pdb=" N ASP H 154 " --> pdb=" O MET H 151 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG H 155 " --> pdb=" O ALA H 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 151 through 155' Processing helix chain 'I' and resid 90 through 102 removed outlier: 3.601A pdb=" N GLN I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 155 removed outlier: 3.775A pdb=" N ASP I 154 " --> pdb=" O MET I 151 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG I 155 " --> pdb=" O ALA I 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 151 through 155' Processing helix chain 'J' and resid 90 through 102 removed outlier: 3.567A pdb=" N GLN J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.768A pdb=" N ASP J 154 " --> pdb=" O MET J 151 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG J 155 " --> pdb=" O ALA J 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 151 through 155' Processing helix chain 'K' and resid 90 through 102 Processing helix chain 'K' and resid 151 through 155 removed outlier: 3.723A pdb=" N ASP K 154 " --> pdb=" O MET K 151 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG K 155 " --> pdb=" O ALA K 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 151 through 155' Processing helix chain 'L' and resid 90 through 102 Processing helix chain 'L' and resid 151 through 155 removed outlier: 3.542A pdb=" N ASP L 154 " --> pdb=" O MET L 151 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG L 155 " --> pdb=" O ALA L 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 151 through 155' Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.511A pdb=" N LEU A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 84 removed outlier: 3.982A pdb=" N LEU A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.881A pdb=" N VAL A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 4.279A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 98' Processing helix chain 'B' and resid 2 through 16 removed outlier: 3.752A pdb=" N LEU B 6 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 removed outlier: 3.688A pdb=" N LEU B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) Proline residue: B 87 - end of helix removed outlier: 4.306A pdb=" N ASP B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 removed outlier: 4.345A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 16 removed outlier: 3.695A pdb=" N ALA C 13 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 82 removed outlier: 3.723A pdb=" N LEU C 77 " --> pdb=" O PRO C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 91 removed outlier: 4.180A pdb=" N VAL C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.516A pdb=" N LEU D 6 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 16 " --> pdb=" O ASP D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 84 removed outlier: 3.674A pdb=" N LEU D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.077A pdb=" N VAL D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP D 91 " --> pdb=" O PRO D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 4.299A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 94 through 98' Processing helix chain 'E' and resid 2 through 16 removed outlier: 3.743A pdb=" N LEU E 6 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 82 removed outlier: 3.742A pdb=" N LEU E 77 " --> pdb=" O PRO E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.934A pdb=" N VAL E 88 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP E 91 " --> pdb=" O PRO E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 removed outlier: 4.365A pdb=" N LEU E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 16 removed outlier: 3.710A pdb=" N ALA F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 16 " --> pdb=" O ASP F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 83 removed outlier: 3.907A pdb=" N LEU F 77 " --> pdb=" O PRO F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 91 removed outlier: 4.105A pdb=" N VAL F 88 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP F 91 " --> pdb=" O PRO F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 removed outlier: 4.173A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 23 removed outlier: 3.694A pdb=" N ALA M 10 " --> pdb=" O ASN M 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 24 removed outlier: 3.632A pdb=" N ALA N 10 " --> pdb=" O ASN N 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 23 removed outlier: 3.728A pdb=" N ALA O 10 " --> pdb=" O ASN O 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 23 removed outlier: 3.703A pdb=" N ALA P 10 " --> pdb=" O ASN P 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 24 removed outlier: 3.667A pdb=" N ALA Q 10 " --> pdb=" O ASN Q 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 23 removed outlier: 3.730A pdb=" N ALA R 10 " --> pdb=" O ASN R 6 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 36 through 39 removed outlier: 4.829A pdb=" N LEU G 17 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA G 107 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL G 124 " --> pdb=" O THR G 144 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N THR G 144 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA G 85 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL G 42 " --> pdb=" O ALA G 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 36 through 39 removed outlier: 4.829A pdb=" N LEU G 17 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA G 107 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 17.875A pdb=" N ARG G 121 " --> pdb=" O ASP L 56 " (cutoff:3.500A) removed outlier: 14.392A pdb=" N ASP L 56 " --> pdb=" O ARG G 121 " (cutoff:3.500A) removed outlier: 12.184A pdb=" N TRP G 123 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N SER L 54 " --> pdb=" O TRP G 123 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N SER G 125 " --> pdb=" O ALA L 52 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR L 51 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS L 75 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU L 53 " --> pdb=" O GLY L 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 50 through 51 removed outlier: 5.060A pdb=" N ALA H 107 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU H 17 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 50 through 51 removed outlier: 5.104A pdb=" N VAL H 124 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N THR H 144 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA H 85 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL H 42 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 54 through 56 Processing sheet with id=AA6, first strand: chain 'H' and resid 50 through 51 removed outlier: 4.975A pdb=" N ALA I 107 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU I 17 " --> pdb=" O LEU I 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 50 through 51 removed outlier: 6.655A pdb=" N LYS I 142 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE I 127 " --> pdb=" O THR I 140 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR I 140 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS I 129 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR I 138 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA I 85 " --> pdb=" O VAL I 42 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL I 42 " --> pdb=" O ALA I 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 56 Processing sheet with id=AA9, first strand: chain 'I' and resid 70 through 76 removed outlier: 5.912A pdb=" N GLU I 53 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS I 75 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR I 51 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER J 125 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N SER I 54 " --> pdb=" O TRP J 123 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N TRP J 123 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 14.353A pdb=" N ASP I 56 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 17.822A pdb=" N ARG J 121 " --> pdb=" O ASP I 56 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA J 107 " --> pdb=" O TYR J 20 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU J 17 " --> pdb=" O LEU J 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 70 through 76 removed outlier: 5.912A pdb=" N GLU I 53 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS I 75 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR I 51 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER J 125 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N SER I 54 " --> pdb=" O TRP J 123 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N TRP J 123 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 14.353A pdb=" N ASP I 56 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 17.822A pdb=" N ARG J 121 " --> pdb=" O ASP I 56 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL J 124 " --> pdb=" O THR J 144 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N THR J 144 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA J 85 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL J 42 " --> pdb=" O ALA J 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 50 through 51 removed outlier: 5.069A pdb=" N ALA K 107 " --> pdb=" O TYR K 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 50 through 51 removed outlier: 5.105A pdb=" N VAL K 124 " --> pdb=" O THR K 144 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N THR K 144 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA K 85 " --> pdb=" O VAL K 42 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL K 42 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 54 through 56 Processing sheet with id=AB5, first strand: chain 'K' and resid 50 through 51 removed outlier: 5.129A pdb=" N ALA L 107 " --> pdb=" O TYR L 20 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 50 through 51 removed outlier: 6.648A pdb=" N LYS L 142 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE L 127 " --> pdb=" O THR L 140 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR L 140 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS L 129 " --> pdb=" O THR L 138 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR L 138 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER L 81 " --> pdb=" O THR L 46 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA L 85 " --> pdb=" O VAL L 42 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL L 42 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 54 through 56 Processing sheet with id=AB8, first strand: chain 'A' and resid 23 through 25 removed outlier: 4.213A pdb=" N ALA A 46 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN A 59 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N SER A 120 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR A 109 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP A 122 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR A 107 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 124 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.816A pdb=" N ALA A 29 " --> pdb=" O ARG O 57 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLU O 59 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE A 31 " --> pdb=" O GLU O 59 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N SER O 61 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 30 through 31 removed outlier: 6.736A pdb=" N PHE B 31 " --> pdb=" O GLU P 59 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N SER P 61 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 40 through 48 removed outlier: 4.262A pdb=" N ALA B 46 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN B 59 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER B 120 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR B 109 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP B 122 " --> pdb=" O TYR B 107 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR B 107 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR B 124 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 22 through 25 removed outlier: 3.571A pdb=" N ALA C 38 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA C 46 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN C 59 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER C 120 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR C 109 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP C 122 " --> pdb=" O TYR C 107 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR C 107 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR C 124 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.752A pdb=" N PHE C 31 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N SER Q 61 " --> pdb=" O PHE C 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 22 through 25 removed outlier: 3.674A pdb=" N ALA D 38 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA D 46 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLN D 59 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N SER D 120 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR D 109 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP D 122 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR D 107 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR D 124 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.616A pdb=" N GLU R 59 " --> pdb=" O PHE D 31 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 23 through 25 removed outlier: 4.239A pdb=" N ALA E 46 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN E 59 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER E 120 " --> pdb=" O TYR E 109 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR E 109 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP E 122 " --> pdb=" O TYR E 107 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR E 107 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR E 124 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 30 through 31 removed outlier: 6.686A pdb=" N PHE E 31 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N SER M 61 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 22 through 25 removed outlier: 3.724A pdb=" N ALA F 38 " --> pdb=" O PHE F 67 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA F 46 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN F 59 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER F 120 " --> pdb=" O TYR F 109 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR F 109 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP F 122 " --> pdb=" O TYR F 107 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR F 107 " --> pdb=" O ASP F 122 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR F 124 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 29 through 32 removed outlier: 7.129A pdb=" N ALA F 29 " --> pdb=" O ARG N 57 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLU N 59 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE F 31 " --> pdb=" O GLU N 59 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N SER N 61 " --> pdb=" O PHE F 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 25 through 31 removed outlier: 8.074A pdb=" N ARG M 40 " --> pdb=" O ARG M 68 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ARG M 68 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N HIS M 102 " --> pdb=" O VAL M 93 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL M 93 " --> pdb=" O HIS M 102 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP M 104 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR M 80 " --> pdb=" O THR M 30 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 25 through 31 removed outlier: 8.145A pdb=" N ARG N 40 " --> pdb=" O ARG N 68 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG N 68 " --> pdb=" O ARG N 40 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS N 102 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL N 93 " --> pdb=" O HIS N 102 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP N 104 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR N 80 " --> pdb=" O THR N 30 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 25 through 31 removed outlier: 8.120A pdb=" N ARG O 40 " --> pdb=" O ARG O 68 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG O 68 " --> pdb=" O ARG O 40 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS O 102 " --> pdb=" O VAL O 93 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL O 93 " --> pdb=" O HIS O 102 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP O 104 " --> pdb=" O ASP O 91 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR O 80 " --> pdb=" O THR O 30 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 25 through 31 removed outlier: 8.178A pdb=" N ARG P 40 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG P 68 " --> pdb=" O ARG P 40 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N HIS P 102 " --> pdb=" O VAL P 93 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL P 93 " --> pdb=" O HIS P 102 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP P 104 " --> pdb=" O ASP P 91 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR P 80 " --> pdb=" O THR P 30 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 38 through 41 removed outlier: 6.907A pdb=" N THR Q 80 " --> pdb=" O THR Q 30 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP Q 104 " --> pdb=" O ASP Q 91 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL Q 93 " --> pdb=" O HIS Q 102 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N HIS Q 102 " --> pdb=" O VAL Q 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 25 through 31 removed outlier: 8.155A pdb=" N ARG R 40 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG R 68 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N HIS R 102 " --> pdb=" O VAL R 93 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL R 93 " --> pdb=" O HIS R 102 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP R 104 " --> pdb=" O ASP R 91 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU R 86 " --> pdb=" O ILE R 83 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR R 80 " --> pdb=" O THR R 30 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2121 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: 6.05 Time building geometry restraints manager: 5.16 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: 6238 1.34 - 1.46: 3561 1.46 - 1.58: 9041 1.58 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 18954 Sorted by residual: bond pdb=" CA ASP B 35 " pdb=" C ASP B 35 " ideal model delta sigma weight residual 1.530 1.499 0.031 1.14e-02 7.69e+03 7.42e+00 bond pdb=" N ALA B 38 " pdb=" CA ALA B 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.97e+00 bond pdb=" CA ALA D 38 " pdb=" C ALA D 38 " ideal model delta sigma weight residual 1.520 1.492 0.029 1.20e-02 6.94e+03 5.66e+00 bond pdb=" C PHE B 36 " pdb=" O PHE B 36 " ideal model delta sigma weight residual 1.244 1.221 0.023 1.00e-02 1.00e+04 5.12e+00 bond pdb=" CA PRO B 37 " pdb=" C PRO B 37 " ideal model delta sigma weight residual 1.517 1.548 -0.031 1.46e-02 4.69e+03 4.53e+00 ... (remaining 18949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 25492 2.56 - 5.12: 288 5.12 - 7.68: 19 7.68 - 10.24: 10 10.24 - 12.80: 3 Bond angle restraints: 25812 Sorted by residual: angle pdb=" N PHE B 36 " pdb=" CA PHE B 36 " pdb=" C PHE B 36 " ideal model delta sigma weight residual 112.35 121.93 -9.58 1.34e+00 5.57e-01 5.11e+01 angle pdb=" C PHE D 36 " pdb=" N PRO D 37 " pdb=" CA PRO D 37 " ideal model delta sigma weight residual 120.23 111.71 8.52 1.23e+00 6.61e-01 4.80e+01 angle pdb=" N GLU A 82 " pdb=" CA GLU A 82 " pdb=" C GLU A 82 " ideal model delta sigma weight residual 111.36 118.22 -6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" N ALA B 38 " pdb=" CA ALA B 38 " pdb=" C ALA B 38 " ideal model delta sigma weight residual 110.80 123.21 -12.41 2.13e+00 2.20e-01 3.40e+01 angle pdb=" N PHE E 36 " pdb=" CA PHE E 36 " pdb=" C PHE E 36 " ideal model delta sigma weight residual 109.81 122.61 -12.80 2.21e+00 2.05e-01 3.36e+01 ... (remaining 25807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10189 17.96 - 35.92: 785 35.92 - 53.88: 144 53.88 - 71.83: 18 71.83 - 89.79: 12 Dihedral angle restraints: 11148 sinusoidal: 4320 harmonic: 6828 Sorted by residual: dihedral pdb=" N PHE E 36 " pdb=" C PHE E 36 " pdb=" CA PHE E 36 " pdb=" CB PHE E 36 " ideal model delta harmonic sigma weight residual 122.80 139.99 -17.19 0 2.50e+00 1.60e-01 4.73e+01 dihedral pdb=" C PHE E 36 " pdb=" N PHE E 36 " pdb=" CA PHE E 36 " pdb=" CB PHE E 36 " ideal model delta harmonic sigma weight residual -122.60 -138.78 16.18 0 2.50e+00 1.60e-01 4.19e+01 dihedral pdb=" N PHE B 36 " pdb=" C PHE B 36 " pdb=" CA PHE B 36 " pdb=" CB PHE B 36 " ideal model delta harmonic sigma weight residual 122.80 137.52 -14.72 0 2.50e+00 1.60e-01 3.47e+01 ... (remaining 11145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 2791 0.161 - 0.322: 10 0.322 - 0.483: 3 0.483 - 0.644: 2 0.644 - 0.805: 2 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CA PHE E 36 " pdb=" N PHE E 36 " pdb=" C PHE E 36 " pdb=" CB PHE E 36 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CA PHE B 36 " pdb=" N PHE B 36 " pdb=" C PHE B 36 " pdb=" CB PHE B 36 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA PHE D 36 " pdb=" N PHE D 36 " pdb=" C PHE D 36 " pdb=" CB PHE D 36 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.05e+00 ... (remaining 2805 not shown) Planarity restraints: 3408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 82 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C GLU C 82 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU C 82 " -0.016 2.00e-02 2.50e+03 pdb=" N SER C 83 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 34 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C ALA D 34 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA D 34 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 35 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 38 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ALA B 38 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA B 38 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 39 " 0.014 2.00e-02 2.50e+03 ... (remaining 3405 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2917 2.76 - 3.29: 16565 3.29 - 3.83: 28558 3.83 - 4.36: 32315 4.36 - 4.90: 60650 Nonbonded interactions: 141005 Sorted by model distance: nonbonded pdb=" NH1 ARG H 148 " pdb=" O PRO H 149 " model vdw 2.224 3.120 nonbonded pdb=" OD2 ASP A 35 " pdb=" NH2 ARG P 115 " model vdw 2.250 3.120 nonbonded pdb=" OD1 ASP K 44 " pdb=" N LEU K 45 " model vdw 2.254 3.120 nonbonded pdb=" OD1 ASP H 44 " pdb=" N LEU H 45 " model vdw 2.255 3.120 nonbonded pdb=" OD2 ASP F 35 " pdb=" NH2 ARG O 115 " model vdw 2.263 3.120 ... (remaining 141000 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 group one per residue 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: 2.690 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: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 41.790 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.006 0.051 18954 Z= 0.397 Angle : 0.693 12.803 25812 Z= 0.377 Chirality : 0.055 0.805 2808 Planarity : 0.004 0.044 3408 Dihedral : 13.201 89.792 6780 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.41 % Allowed : 0.31 % Favored : 99.28 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2358 helix: 1.35 (0.30), residues: 306 sheet: 0.07 (0.18), residues: 822 loop : -1.48 (0.14), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 99 HIS 0.005 0.001 HIS E 17 PHE 0.039 0.002 PHE A 36 TYR 0.013 0.002 TYR B 129 ARG 0.008 0.001 ARG M 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 504 time to evaluate : 2.086 Fit side-chains revert: symmetry clash REVERT: G 142 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8421 (ttpp) REVERT: I 59 TYR cc_start: 0.7949 (m-80) cc_final: 0.7662 (m-10) REVERT: I 142 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8480 (ttpp) REVERT: J 139 ARG cc_start: 0.9178 (tpp-160) cc_final: 0.8913 (ttm-80) REVERT: L 21 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7896 (pttm) REVERT: L 59 TYR cc_start: 0.7870 (m-80) cc_final: 0.7640 (m-10) REVERT: L 87 MET cc_start: 0.7541 (mtp) cc_final: 0.6920 (mtm) REVERT: L 151 MET cc_start: 0.8621 (mmm) cc_final: 0.8319 (mmp) REVERT: A 4 THR cc_start: 0.8523 (m) cc_final: 0.7953 (p) REVERT: C 76 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7346 (tm-30) REVERT: D 4 THR cc_start: 0.8616 (m) cc_final: 0.8065 (p) REVERT: D 35 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6797 (p0) REVERT: E 19 THR cc_start: 0.5995 (m) cc_final: 0.5675 (m) REVERT: E 80 TRP cc_start: 0.8607 (OUTLIER) cc_final: 0.6517 (t60) REVERT: F 18 ASP cc_start: 0.5926 (t70) cc_final: 0.5706 (m-30) REVERT: M 70 ASP cc_start: 0.8295 (m-30) cc_final: 0.8090 (m-30) REVERT: O 79 ASP cc_start: 0.7988 (m-30) cc_final: 0.7655 (m-30) REVERT: Q 25 THR cc_start: 0.8121 (t) cc_final: 0.7916 (t) REVERT: Q 39 ILE cc_start: 0.9122 (mt) cc_final: 0.8839 (mt) REVERT: R 79 ASP cc_start: 0.7986 (m-30) cc_final: 0.7665 (m-30) REVERT: R 91 ASP cc_start: 0.8872 (t0) cc_final: 0.8147 (t0) outliers start: 8 outliers final: 0 residues processed: 512 average time/residue: 0.3581 time to fit residues: 262.2227 Evaluate side-chains 355 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 353 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain E residue 80 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 91 GLN I 101 ASN ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN A 17 HIS C 17 HIS F 59 GLN N 6 ASN P 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18954 Z= 0.277 Angle : 0.614 7.938 25812 Z= 0.323 Chirality : 0.047 0.233 2808 Planarity : 0.004 0.042 3408 Dihedral : 4.989 53.413 2614 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.45 % Allowed : 9.92 % Favored : 87.63 % 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: -0.72 (0.16), residues: 2358 helix: 0.85 (0.27), residues: 348 sheet: 0.01 (0.17), residues: 894 loop : -1.31 (0.15), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 80 HIS 0.004 0.001 HIS F 63 PHE 0.034 0.002 PHE C 36 TYR 0.017 0.001 TYR L 55 ARG 0.005 0.000 ARG G 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 382 time to evaluate : 2.086 Fit side-chains REVERT: G 142 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8387 (ttpp) REVERT: K 102 GLU cc_start: 0.7184 (pp20) cc_final: 0.6869 (pp20) REVERT: L 59 TYR cc_start: 0.8038 (m-80) cc_final: 0.7724 (m-10) REVERT: C 18 ASP cc_start: 0.5859 (t70) cc_final: 0.5629 (m-30) REVERT: E 80 TRP cc_start: 0.8807 (OUTLIER) cc_final: 0.6659 (t60) REVERT: O 73 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7372 (tpp-160) REVERT: O 86 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7073 (mt-10) REVERT: P 34 GLN cc_start: 0.8478 (mt0) cc_final: 0.8165 (mt0) REVERT: R 86 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7143 (mt-10) REVERT: R 103 LEU cc_start: 0.8892 (mp) cc_final: 0.8563 (mp) outliers start: 48 outliers final: 38 residues processed: 406 average time/residue: 0.3294 time to fit residues: 197.9533 Evaluate side-chains 372 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 333 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 94 SER Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain R residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 211 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 101 ASN I 101 ASN ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS P 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18954 Z= 0.170 Angle : 0.539 6.999 25812 Z= 0.283 Chirality : 0.045 0.202 2808 Planarity : 0.004 0.044 3408 Dihedral : 4.656 52.831 2612 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.78 % Favored : 98.18 % Rotamer: Outliers : 2.81 % Allowed : 12.58 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2358 helix: 0.93 (0.27), residues: 348 sheet: 0.23 (0.16), residues: 996 loop : -1.25 (0.16), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 86 HIS 0.011 0.001 HIS A 17 PHE 0.027 0.001 PHE C 36 TYR 0.009 0.001 TYR I 55 ARG 0.006 0.000 ARG J 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 362 time to evaluate : 2.145 Fit side-chains REVERT: G 118 ASP cc_start: 0.8144 (t0) cc_final: 0.7789 (t0) REVERT: G 142 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8398 (ttpp) REVERT: H 8 MET cc_start: 0.7576 (mtm) cc_final: 0.7314 (mtt) REVERT: K 7 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8559 (t) REVERT: K 102 GLU cc_start: 0.7314 (pp20) cc_final: 0.6922 (pp20) REVERT: L 59 TYR cc_start: 0.8058 (m-80) cc_final: 0.7830 (m-80) REVERT: C 80 TRP cc_start: 0.8767 (OUTLIER) cc_final: 0.6322 (t60) REVERT: E 80 TRP cc_start: 0.8746 (OUTLIER) cc_final: 0.6490 (t60) REVERT: P 39 ILE cc_start: 0.9049 (mt) cc_final: 0.8686 (mm) REVERT: R 86 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7047 (mt-10) REVERT: R 91 ASP cc_start: 0.8916 (t0) cc_final: 0.8239 (t0) REVERT: R 103 LEU cc_start: 0.8868 (mp) cc_final: 0.8565 (mp) outliers start: 55 outliers final: 46 residues processed: 392 average time/residue: 0.3287 time to fit residues: 191.3040 Evaluate side-chains 383 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 334 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 80 TRP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 94 SER Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain R residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 GLN ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN A 17 HIS M 6 ASN P 6 ASN Q 6 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 18954 Z= 0.558 Angle : 0.722 8.609 25812 Z= 0.382 Chirality : 0.052 0.299 2808 Planarity : 0.006 0.043 3408 Dihedral : 5.478 58.910 2612 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 4.60 % Allowed : 14.21 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.16), residues: 2358 helix: 0.38 (0.27), residues: 348 sheet: 0.04 (0.17), residues: 876 loop : -1.41 (0.15), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 80 HIS 0.006 0.002 HIS E 17 PHE 0.041 0.003 PHE C 36 TYR 0.020 0.002 TYR E 129 ARG 0.006 0.001 ARG G 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 312 time to evaluate : 2.158 Fit side-chains REVERT: G 142 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8346 (ttpp) REVERT: H 8 MET cc_start: 0.7770 (mtm) cc_final: 0.7483 (mtt) REVERT: I 102 GLU cc_start: 0.7612 (pp20) cc_final: 0.7287 (pp20) REVERT: J 75 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8726 (mttm) REVERT: K 102 GLU cc_start: 0.7545 (pp20) cc_final: 0.7049 (pp20) REVERT: L 59 TYR cc_start: 0.8132 (m-80) cc_final: 0.7866 (m-80) REVERT: L 87 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7740 (mtm) REVERT: E 80 TRP cc_start: 0.9028 (OUTLIER) cc_final: 0.7005 (t60) REVERT: O 91 ASP cc_start: 0.8977 (t0) cc_final: 0.8183 (t0) REVERT: P 34 GLN cc_start: 0.8497 (mt0) cc_final: 0.8212 (mt0) REVERT: Q 54 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7691 (mp10) outliers start: 90 outliers final: 66 residues processed: 370 average time/residue: 0.3391 time to fit residues: 184.6796 Evaluate side-chains 364 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 294 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 148 ARG Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 54 GLN Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 168 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN M 6 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18954 Z= 0.188 Angle : 0.545 6.971 25812 Z= 0.286 Chirality : 0.045 0.198 2808 Planarity : 0.004 0.043 3408 Dihedral : 4.900 57.734 2612 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.30 % Rotamer: Outliers : 3.02 % Allowed : 16.36 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2358 helix: 0.68 (0.27), residues: 348 sheet: 0.12 (0.16), residues: 1026 loop : -1.25 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 80 HIS 0.002 0.001 HIS N 102 PHE 0.027 0.002 PHE C 36 TYR 0.011 0.001 TYR F 42 ARG 0.007 0.000 ARG J 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 346 time to evaluate : 2.095 Fit side-chains REVERT: G 118 ASP cc_start: 0.8351 (t0) cc_final: 0.8070 (t0) REVERT: G 142 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8441 (ttpp) REVERT: H 8 MET cc_start: 0.7719 (mtm) cc_final: 0.7475 (mtt) REVERT: I 102 GLU cc_start: 0.7429 (pp20) cc_final: 0.7147 (pp20) REVERT: J 75 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8609 (mttm) REVERT: K 7 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8535 (t) REVERT: K 102 GLU cc_start: 0.7434 (pp20) cc_final: 0.7024 (pp20) REVERT: L 59 TYR cc_start: 0.8122 (m-80) cc_final: 0.7836 (m-80) REVERT: L 151 MET cc_start: 0.8767 (mmm) cc_final: 0.8566 (mmp) REVERT: B 125 TYR cc_start: 0.8925 (m-80) cc_final: 0.8683 (m-80) REVERT: E 80 TRP cc_start: 0.8863 (OUTLIER) cc_final: 0.6714 (t60) REVERT: M 34 GLN cc_start: 0.8534 (mt0) cc_final: 0.8255 (mt0) REVERT: O 86 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6878 (mt-10) REVERT: O 91 ASP cc_start: 0.8945 (t0) cc_final: 0.8208 (t0) REVERT: O 103 LEU cc_start: 0.9002 (mp) cc_final: 0.8778 (mp) REVERT: R 91 ASP cc_start: 0.8839 (t0) cc_final: 0.7896 (t0) outliers start: 59 outliers final: 45 residues processed: 382 average time/residue: 0.3277 time to fit residues: 185.9437 Evaluate side-chains 377 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 329 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 148 ARG Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 132 optimal weight: 0.0980 chunk 55 optimal weight: 10.0000 chunk 226 optimal weight: 0.0470 chunk 187 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.6284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN M 6 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18954 Z= 0.188 Angle : 0.537 7.299 25812 Z= 0.280 Chirality : 0.045 0.197 2808 Planarity : 0.004 0.043 3408 Dihedral : 4.646 57.671 2612 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.78 % Favored : 98.18 % Rotamer: Outliers : 3.83 % Allowed : 16.05 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2358 helix: 0.80 (0.27), residues: 348 sheet: 0.26 (0.17), residues: 876 loop : -1.28 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 80 HIS 0.002 0.001 HIS C 63 PHE 0.027 0.001 PHE C 36 TYR 0.013 0.001 TYR L 20 ARG 0.007 0.000 ARG J 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 350 time to evaluate : 2.335 Fit side-chains REVERT: G 102 GLU cc_start: 0.7767 (pp20) cc_final: 0.7535 (pp20) REVERT: G 118 ASP cc_start: 0.8341 (t0) cc_final: 0.7930 (t0) REVERT: J 75 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8584 (mttm) REVERT: J 84 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8989 (pp) REVERT: J 90 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6805 (tp30) REVERT: K 7 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8537 (t) REVERT: K 102 GLU cc_start: 0.7586 (pp20) cc_final: 0.7148 (pp20) REVERT: L 59 TYR cc_start: 0.8124 (m-80) cc_final: 0.7840 (m-80) REVERT: B 125 TYR cc_start: 0.8908 (m-80) cc_final: 0.8682 (m-80) REVERT: C 33 GLU cc_start: 0.7746 (mp0) cc_final: 0.7545 (mm-30) REVERT: E 80 TRP cc_start: 0.8891 (OUTLIER) cc_final: 0.6848 (t60) REVERT: F 6 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8239 (tt) REVERT: M 34 GLN cc_start: 0.8547 (mt0) cc_final: 0.8232 (mt0) REVERT: M 71 GLU cc_start: 0.7318 (pt0) cc_final: 0.6921 (pt0) REVERT: O 103 LEU cc_start: 0.8983 (mp) cc_final: 0.8748 (mp) REVERT: Q 47 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: Q 103 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8712 (mp) outliers start: 75 outliers final: 59 residues processed: 396 average time/residue: 0.3209 time to fit residues: 190.8466 Evaluate side-chains 406 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 339 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 148 ARG Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18954 Z= 0.302 Angle : 0.586 7.508 25812 Z= 0.307 Chirality : 0.046 0.225 2808 Planarity : 0.005 0.041 3408 Dihedral : 4.872 59.948 2612 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % Rotamer: Outliers : 4.40 % Allowed : 16.36 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2358 helix: 0.74 (0.27), residues: 348 sheet: 0.18 (0.17), residues: 876 loop : -1.29 (0.15), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 80 HIS 0.002 0.001 HIS E 17 PHE 0.030 0.002 PHE C 36 TYR 0.013 0.001 TYR L 55 ARG 0.008 0.000 ARG G 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 329 time to evaluate : 2.262 Fit side-chains REVERT: G 102 GLU cc_start: 0.7704 (pp20) cc_final: 0.7481 (pp20) REVERT: G 118 ASP cc_start: 0.8403 (t0) cc_final: 0.7994 (t0) REVERT: H 8 MET cc_start: 0.7730 (mtm) cc_final: 0.7507 (mtt) REVERT: H 84 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8951 (pp) REVERT: J 75 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8804 (mttm) REVERT: J 84 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9038 (pp) REVERT: J 90 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6850 (tp30) REVERT: K 7 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8545 (t) REVERT: K 102 GLU cc_start: 0.7658 (pp20) cc_final: 0.7186 (pp20) REVERT: L 59 TYR cc_start: 0.8135 (m-80) cc_final: 0.7920 (m-80) REVERT: L 151 MET cc_start: 0.8796 (mmm) cc_final: 0.8498 (mmp) REVERT: A 6 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8125 (tt) REVERT: D 6 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8152 (tt) REVERT: E 80 TRP cc_start: 0.8996 (OUTLIER) cc_final: 0.7122 (t60) REVERT: F 6 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8305 (tt) REVERT: M 34 GLN cc_start: 0.8582 (mt0) cc_final: 0.8279 (mt0) REVERT: N 73 ARG cc_start: 0.7693 (ttm110) cc_final: 0.7312 (ttm-80) REVERT: P 34 GLN cc_start: 0.8307 (mt0) cc_final: 0.8107 (mt0) REVERT: Q 47 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7774 (tt0) outliers start: 86 outliers final: 64 residues processed: 384 average time/residue: 0.3132 time to fit residues: 180.3902 Evaluate side-chains 394 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 320 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 148 ARG Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 143 optimal weight: 0.0570 chunk 153 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN K 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 18954 Z= 0.397 Angle : 0.642 9.583 25812 Z= 0.339 Chirality : 0.049 0.254 2808 Planarity : 0.005 0.041 3408 Dihedral : 5.208 56.635 2612 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.21 % Favored : 97.75 % Rotamer: Outliers : 4.86 % Allowed : 16.16 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2358 helix: 0.50 (0.27), residues: 348 sheet: 0.07 (0.17), residues: 876 loop : -1.35 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 80 HIS 0.003 0.001 HIS N 102 PHE 0.035 0.002 PHE F 36 TYR 0.017 0.002 TYR I 55 ARG 0.009 0.001 ARG J 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 306 time to evaluate : 2.152 Fit side-chains REVERT: G 102 GLU cc_start: 0.7803 (pp20) cc_final: 0.7540 (pp20) REVERT: G 118 ASP cc_start: 0.8456 (t0) cc_final: 0.8190 (t0) REVERT: H 8 MET cc_start: 0.7775 (mtm) cc_final: 0.7574 (mtt) REVERT: H 84 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9048 (pp) REVERT: J 84 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9138 (pp) REVERT: K 7 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8538 (t) REVERT: K 102 GLU cc_start: 0.7634 (pp20) cc_final: 0.7166 (pp20) REVERT: L 59 TYR cc_start: 0.8136 (m-80) cc_final: 0.7935 (m-80) REVERT: L 87 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7667 (mtm) REVERT: L 151 MET cc_start: 0.8800 (mmm) cc_final: 0.8572 (mmp) REVERT: A 6 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8174 (tt) REVERT: D 6 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8182 (tt) REVERT: D 117 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9188 (tp) REVERT: E 80 TRP cc_start: 0.9064 (OUTLIER) cc_final: 0.6838 (t60) REVERT: F 6 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8390 (tt) REVERT: N 73 ARG cc_start: 0.7794 (ttm110) cc_final: 0.7411 (ttm-80) REVERT: Q 47 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: Q 103 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8808 (mp) outliers start: 95 outliers final: 71 residues processed: 368 average time/residue: 0.3262 time to fit residues: 178.2426 Evaluate side-chains 382 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 300 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 148 ARG Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 189 optimal weight: 0.0670 chunk 198 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18954 Z= 0.226 Angle : 0.567 7.391 25812 Z= 0.297 Chirality : 0.046 0.197 2808 Planarity : 0.004 0.042 3408 Dihedral : 4.858 58.192 2612 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.82 % Favored : 98.13 % Rotamer: Outliers : 4.29 % Allowed : 17.18 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2358 helix: 0.70 (0.28), residues: 348 sheet: 0.15 (0.17), residues: 864 loop : -1.32 (0.16), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 80 HIS 0.002 0.001 HIS B 63 PHE 0.032 0.002 PHE C 36 TYR 0.011 0.001 TYR I 55 ARG 0.009 0.000 ARG G 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 327 time to evaluate : 2.202 Fit side-chains REVERT: G 102 GLU cc_start: 0.7798 (pp20) cc_final: 0.7538 (pp20) REVERT: G 118 ASP cc_start: 0.8385 (t0) cc_final: 0.7959 (t0) REVERT: H 8 MET cc_start: 0.7720 (mtm) cc_final: 0.7511 (mtt) REVERT: H 84 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8933 (pp) REVERT: J 84 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9048 (pp) REVERT: K 7 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8528 (t) REVERT: K 102 GLU cc_start: 0.7682 (pp20) cc_final: 0.7269 (pp20) REVERT: L 87 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7610 (mtm) REVERT: L 151 MET cc_start: 0.8743 (mmm) cc_final: 0.8527 (mmp) REVERT: C 6 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8276 (tt) REVERT: D 6 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8168 (tt) REVERT: D 117 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9168 (tp) REVERT: E 80 TRP cc_start: 0.8991 (OUTLIER) cc_final: 0.6949 (t60) REVERT: F 6 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8339 (tt) REVERT: M 45 ASP cc_start: 0.8901 (t0) cc_final: 0.8679 (t0) REVERT: N 73 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7482 (ttm-80) REVERT: Q 47 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: Q 103 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8773 (mp) outliers start: 84 outliers final: 64 residues processed: 379 average time/residue: 0.3147 time to fit residues: 180.4420 Evaluate side-chains 397 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 322 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 148 ARG Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain R residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.0770 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 154 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 overall best weight: 2.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 101 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18954 Z= 0.235 Angle : 0.566 7.562 25812 Z= 0.297 Chirality : 0.046 0.198 2808 Planarity : 0.004 0.041 3408 Dihedral : 4.810 57.615 2612 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.87 % Favored : 98.09 % Rotamer: Outliers : 4.40 % Allowed : 17.28 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2358 helix: 0.70 (0.28), residues: 348 sheet: 0.18 (0.17), residues: 864 loop : -1.30 (0.16), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 80 HIS 0.002 0.001 HIS N 102 PHE 0.028 0.002 PHE F 36 TYR 0.013 0.001 TYR I 20 ARG 0.006 0.000 ARG J 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 326 time to evaluate : 2.299 Fit side-chains REVERT: G 102 GLU cc_start: 0.7814 (pp20) cc_final: 0.7545 (pp20) REVERT: G 118 ASP cc_start: 0.8385 (t0) cc_final: 0.7961 (t0) REVERT: H 8 MET cc_start: 0.7727 (mtm) cc_final: 0.7500 (mtt) REVERT: H 84 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8918 (pp) REVERT: J 84 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8988 (pp) REVERT: J 102 GLU cc_start: 0.7618 (pp20) cc_final: 0.7362 (pp20) REVERT: K 7 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8308 (t) REVERT: K 102 GLU cc_start: 0.7704 (pp20) cc_final: 0.7294 (pp20) REVERT: L 59 TYR cc_start: 0.7869 (m-80) cc_final: 0.7642 (m-80) REVERT: L 87 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7620 (mtm) REVERT: L 102 GLU cc_start: 0.7633 (pp20) cc_final: 0.7417 (pp20) REVERT: L 151 MET cc_start: 0.8752 (mmm) cc_final: 0.8547 (mmp) REVERT: A 6 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8191 (tt) REVERT: B 125 TYR cc_start: 0.8915 (m-80) cc_final: 0.8680 (m-80) REVERT: C 6 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8176 (tt) REVERT: D 6 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8122 (tt) REVERT: D 117 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9205 (tp) REVERT: E 80 TRP cc_start: 0.9006 (OUTLIER) cc_final: 0.6902 (t60) REVERT: F 6 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8344 (tt) REVERT: M 70 ASP cc_start: 0.8154 (m-30) cc_final: 0.7884 (m-30) REVERT: N 73 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7496 (ttm-80) REVERT: Q 47 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: Q 103 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8766 (mp) outliers start: 86 outliers final: 70 residues processed: 377 average time/residue: 0.3238 time to fit residues: 185.1169 Evaluate side-chains 404 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 322 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 TRP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain M residue 44 ASP Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 5 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain R residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 101 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093159 restraints weight = 34835.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.095186 restraints weight = 19335.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096559 restraints weight = 12490.623| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18954 Z= 0.239 Angle : 0.562 7.216 25812 Z= 0.295 Chirality : 0.046 0.192 2808 Planarity : 0.004 0.042 3408 Dihedral : 4.796 57.401 2612 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.08 % Favored : 97.88 % Rotamer: Outliers : 4.40 % Allowed : 17.28 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2358 helix: 0.71 (0.28), residues: 348 sheet: 0.20 (0.17), residues: 864 loop : -1.31 (0.16), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 80 HIS 0.003 0.001 HIS N 102 PHE 0.028 0.002 PHE F 36 TYR 0.015 0.001 TYR L 55 ARG 0.009 0.000 ARG J 121 =============================================================================== Job complete usr+sys time: 3930.38 seconds wall clock time: 72 minutes 30.98 seconds (4350.98 seconds total)