Starting phenix.real_space_refine on Wed Nov 20 02:12:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/11_2024/8hla_34859.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/11_2024/8hla_34859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/11_2024/8hla_34859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/11_2024/8hla_34859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/11_2024/8hla_34859.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/11_2024/8hla_34859.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 13596 2.51 5 N 3372 2.21 5 O 3840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20868 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "C" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "D" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "E" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "F" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "G" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "H" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "I" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "J" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "K" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "L" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.09, per 1000 atoms: 0.72 Number of scatterers: 20868 At special positions: 0 Unit cell: (163.777, 160.485, 71.601, 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 3840 8.00 N 3372 7.00 C 13596 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.53 Conformation dependent library (CDL) restraints added in 2.8 seconds 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4824 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 25 sheets defined 37.9% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 4.038A pdb=" N ALA A 27 " --> pdb=" O PRO A 23 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN A 29 " --> pdb=" O TYR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 74 through 89 Processing helix chain 'A' and resid 103 through 109 Processing helix chain 'A' and resid 145 through 162 Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.119A pdb=" N GLN B 29 " --> pdb=" O TYR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.596A pdb=" N PHE B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 90 removed outlier: 5.960A pdb=" N LYS B 80 " --> pdb=" O CYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 109 Processing helix chain 'B' and resid 145 through 163 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'C' and resid 22 through 28 removed outlier: 4.338A pdb=" N PHE C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.726A pdb=" N LEU C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 89 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 145 through 163 Processing helix chain 'C' and resid 187 through 201 Processing helix chain 'D' and resid 22 through 26 removed outlier: 3.883A pdb=" N PHE D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 26' Processing helix chain 'D' and resid 42 through 63 removed outlier: 4.884A pdb=" N ASP D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLN D 59 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 89 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 145 through 163 removed outlier: 3.707A pdb=" N ASP D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 removed outlier: 3.584A pdb=" N GLU D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 26 removed outlier: 4.319A pdb=" N PHE E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 22 through 26' Processing helix chain 'E' and resid 43 through 56 Processing helix chain 'E' and resid 56 through 62 Processing helix chain 'E' and resid 78 through 89 Processing helix chain 'E' and resid 103 through 109 Processing helix chain 'E' and resid 145 through 163 Processing helix chain 'E' and resid 187 through 199 Processing helix chain 'F' and resid 22 through 29 removed outlier: 3.795A pdb=" N PHE F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA F 27 " --> pdb=" O PRO F 23 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 56 Processing helix chain 'F' and resid 56 through 62 Processing helix chain 'F' and resid 74 through 89 Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 145 through 163 Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'G' and resid 22 through 29 removed outlier: 3.947A pdb=" N PHE G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA G 27 " --> pdb=" O PRO G 23 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN G 29 " --> pdb=" O TYR G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 56 Processing helix chain 'G' and resid 56 through 63 removed outlier: 3.579A pdb=" N LEU G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 89 removed outlier: 3.733A pdb=" N GLU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 145 through 162 removed outlier: 3.515A pdb=" N ASP G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 194 Processing helix chain 'H' and resid 22 through 26 removed outlier: 4.185A pdb=" N PHE H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 22 through 26' Processing helix chain 'H' and resid 27 through 30 Processing helix chain 'H' and resid 43 through 56 Processing helix chain 'H' and resid 56 through 63 Processing helix chain 'H' and resid 74 through 89 Processing helix chain 'H' and resid 103 through 109 Processing helix chain 'H' and resid 145 through 163 Processing helix chain 'H' and resid 187 through 201 Processing helix chain 'I' and resid 22 through 26 removed outlier: 3.916A pdb=" N PHE I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 22 through 26' Processing helix chain 'I' and resid 43 through 56 Processing helix chain 'I' and resid 56 through 62 Processing helix chain 'I' and resid 74 through 89 removed outlier: 6.182A pdb=" N LYS I 80 " --> pdb=" O CYS I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 110 Processing helix chain 'I' and resid 145 through 162 Processing helix chain 'I' and resid 187 through 201 Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 43 through 56 Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'J' and resid 74 through 89 removed outlier: 5.937A pdb=" N LYS J 80 " --> pdb=" O CYS J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 109 Processing helix chain 'J' and resid 145 through 162 Processing helix chain 'J' and resid 187 through 199 removed outlier: 3.540A pdb=" N ALA J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 26 removed outlier: 4.227A pdb=" N PHE K 26 " --> pdb=" O LEU K 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 22 through 26' Processing helix chain 'K' and resid 43 through 56 Processing helix chain 'K' and resid 56 through 63 removed outlier: 3.894A pdb=" N LEU K 63 " --> pdb=" O GLN K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 89 Processing helix chain 'K' and resid 103 through 109 removed outlier: 3.571A pdb=" N LYS K 108 " --> pdb=" O GLU K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 163 Processing helix chain 'K' and resid 187 through 200 Processing helix chain 'L' and resid 22 through 26 Processing helix chain 'L' and resid 44 through 56 Processing helix chain 'L' and resid 56 through 63 removed outlier: 3.684A pdb=" N PHE L 60 " --> pdb=" O ARG L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 89 Processing helix chain 'L' and resid 103 through 109 Processing helix chain 'L' and resid 145 through 162 Processing helix chain 'L' and resid 188 through 191 Processing helix chain 'L' and resid 192 through 197 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.528A pdb=" N TRP A 32 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A 68 " --> pdb=" O TRP A 32 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 34 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG A 121 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR A 137 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 123 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 135 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 125 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 125 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE B 135 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 123 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR B 137 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ARG B 121 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP B 32 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 68 " --> pdb=" O TRP B 32 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL B 34 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 70 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE B 36 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE B 98 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY B 69 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 181 removed outlier: 3.685A pdb=" N GLU A 204 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 12 through 15 Processing sheet with id=AA4, first strand: chain 'B' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'C' and resid 12 through 15 Processing sheet with id=AA6, first strand: chain 'C' and resid 97 through 98 removed outlier: 8.399A pdb=" N ILE C 98 " --> pdb=" O PRO C 67 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY C 69 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP C 32 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE C 68 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 34 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 70 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE C 36 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 122 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG C 121 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR C 137 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL C 123 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE C 135 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 125 " --> pdb=" O ARG C 133 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE D 125 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE D 135 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 123 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR D 137 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG D 121 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP D 32 " --> pdb=" O GLU D 66 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE D 68 " --> pdb=" O TRP D 32 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 34 " --> pdb=" O ILE D 68 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU D 70 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE D 36 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ILE D 98 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY D 69 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS D 14 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AA8, first strand: chain 'D' and resid 180 through 181 Processing sheet with id=AA9, first strand: chain 'E' and resid 12 through 15 removed outlier: 3.567A pdb=" N GLY E 18 " --> pdb=" O THR E 15 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 97 through 99 removed outlier: 7.908A pdb=" N ILE E 98 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY E 69 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP E 32 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE E 68 " --> pdb=" O TRP E 32 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL E 34 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU E 70 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE E 36 " --> pdb=" O LEU E 70 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG E 121 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR E 137 " --> pdb=" O ARG E 121 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 123 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE E 135 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE E 125 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA F 134 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP F 32 " --> pdb=" O GLU F 66 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE F 68 " --> pdb=" O TRP F 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL F 34 " --> pdb=" O ILE F 68 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU F 70 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE F 36 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE F 98 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY F 69 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS F 14 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 180 through 181 Processing sheet with id=AB3, first strand: chain 'F' and resid 203 through 205 Processing sheet with id=AB4, first strand: chain 'G' and resid 12 through 15 Processing sheet with id=AB5, first strand: chain 'G' and resid 97 through 99 removed outlier: 8.082A pdb=" N ILE G 98 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY G 69 " --> pdb=" O ILE G 98 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TRP G 32 " --> pdb=" O GLU G 66 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE G 68 " --> pdb=" O TRP G 32 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL G 34 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU G 70 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE G 36 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG G 121 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR G 137 " --> pdb=" O ARG G 121 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL G 123 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE G 135 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE G 125 " --> pdb=" O ARG G 133 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE H 125 " --> pdb=" O ARG H 133 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE H 135 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL H 123 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR H 137 " --> pdb=" O ARG H 121 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ARG H 121 " --> pdb=" O TYR H 137 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP H 32 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE H 68 " --> pdb=" O TRP H 32 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL H 34 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU H 70 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE H 36 " --> pdb=" O LEU H 70 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE H 98 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY H 69 " --> pdb=" O ILE H 98 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS H 14 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 204 through 205 Processing sheet with id=AB7, first strand: chain 'H' and resid 180 through 181 Processing sheet with id=AB8, first strand: chain 'I' and resid 12 through 15 removed outlier: 3.984A pdb=" N GLY I 18 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 97 through 99 removed outlier: 6.565A pdb=" N GLY I 69 " --> pdb=" O ILE I 98 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL I 34 " --> pdb=" O ILE I 68 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU I 70 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE I 36 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG I 121 " --> pdb=" O TYR I 137 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR I 137 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL I 123 " --> pdb=" O ILE I 135 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE I 135 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE I 125 " --> pdb=" O ARG I 133 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA J 134 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP J 32 " --> pdb=" O GLU J 66 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE J 68 " --> pdb=" O TRP J 32 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL J 34 " --> pdb=" O ILE J 68 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU J 70 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE J 36 " --> pdb=" O LEU J 70 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE J 98 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY J 69 " --> pdb=" O ILE J 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 180 through 181 Processing sheet with id=AC2, first strand: chain 'J' and resid 12 through 15 Processing sheet with id=AC3, first strand: chain 'J' and resid 203 through 205 removed outlier: 3.736A pdb=" N GLU J 204 " --> pdb=" O TYR J 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.487A pdb=" N LYS K 14 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ILE K 98 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY K 69 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP K 32 " --> pdb=" O GLU K 66 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE K 68 " --> pdb=" O TRP K 32 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL K 34 " --> pdb=" O ILE K 68 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU K 70 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE K 36 " --> pdb=" O LEU K 70 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG K 121 " --> pdb=" O TYR K 137 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR K 137 " --> pdb=" O ARG K 121 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL K 123 " --> pdb=" O ILE K 135 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE K 135 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE K 125 " --> pdb=" O ARG K 133 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ARG K 133 " --> pdb=" O PRO L 139 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE L 125 " --> pdb=" O ARG L 133 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE L 135 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL L 123 " --> pdb=" O ILE L 135 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR L 137 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG L 121 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP L 32 " --> pdb=" O GLU L 66 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE L 68 " --> pdb=" O TRP L 32 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL L 34 " --> pdb=" O ILE L 68 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU L 70 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE L 36 " --> pdb=" O LEU L 70 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE L 98 " --> pdb=" O PRO L 67 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY L 69 " --> pdb=" O ILE L 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 180 through 181 Processing sheet with id=AC6, first strand: chain 'L' and resid 12 through 15 removed outlier: 3.980A pdb=" N GLY L 18 " --> pdb=" O THR L 15 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 181 through 182 removed outlier: 4.494A pdb=" N SER L 211 " --> pdb=" O VAL L 182 " (cutoff:3.500A) 797 hydrogen bonds defined for protein. 2292 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: 6.07 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6337 1.33 - 1.45: 3584 1.45 - 1.57: 11391 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 21420 Sorted by residual: bond pdb=" C TYR I 137 " pdb=" N TYR I 138 " ideal model delta sigma weight residual 1.331 1.287 0.044 1.48e-02 4.57e+03 8.79e+00 bond pdb=" C TYR A 137 " pdb=" N TYR A 138 " ideal model delta sigma weight residual 1.329 1.277 0.052 1.86e-02 2.89e+03 7.87e+00 bond pdb=" CA ARG B 121 " pdb=" CB ARG B 121 " ideal model delta sigma weight residual 1.536 1.433 0.103 4.10e-02 5.95e+02 6.29e+00 bond pdb=" CG1 ILE A 79 " pdb=" CD1 ILE A 79 " ideal model delta sigma weight residual 1.513 1.417 0.096 3.90e-02 6.57e+02 6.12e+00 bond pdb=" C TYR K 137 " pdb=" N TYR K 138 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.47e-02 4.63e+03 6.00e+00 ... (remaining 21415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 28258 2.56 - 5.11: 722 5.11 - 7.67: 66 7.67 - 10.22: 12 10.22 - 12.78: 6 Bond angle restraints: 29064 Sorted by residual: angle pdb=" C GLN A 193 " pdb=" N ARG A 194 " pdb=" CA ARG A 194 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.83e+01 angle pdb=" N GLY A 201 " pdb=" CA GLY A 201 " pdb=" C GLY A 201 " ideal model delta sigma weight residual 114.95 108.29 6.66 1.41e+00 5.03e-01 2.23e+01 angle pdb=" N LYS F 192 " pdb=" CA LYS F 192 " pdb=" C LYS F 192 " ideal model delta sigma weight residual 113.18 107.28 5.90 1.33e+00 5.65e-01 1.97e+01 angle pdb=" N ILE G 79 " pdb=" CA ILE G 79 " pdb=" C ILE G 79 " ideal model delta sigma weight residual 112.29 108.17 4.12 9.40e-01 1.13e+00 1.92e+01 angle pdb=" N ARG A 194 " pdb=" CA ARG A 194 " pdb=" C ARG A 194 " ideal model delta sigma weight residual 110.80 120.09 -9.29 2.13e+00 2.20e-01 1.90e+01 ... (remaining 29059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 11374 17.52 - 35.04: 1050 35.04 - 52.56: 198 52.56 - 70.08: 30 70.08 - 87.60: 20 Dihedral angle restraints: 12672 sinusoidal: 5208 harmonic: 7464 Sorted by residual: dihedral pdb=" CA GLN A 193 " pdb=" C GLN A 193 " pdb=" N ARG A 194 " pdb=" CA ARG A 194 " ideal model delta harmonic sigma weight residual -180.00 -129.59 -50.41 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA GLY A 103 " pdb=" C GLY A 103 " pdb=" N GLU A 104 " pdb=" CA GLU A 104 " ideal model delta harmonic sigma weight residual -180.00 -143.98 -36.02 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N PRO B 23 " pdb=" CA PRO B 23 " ideal model delta harmonic sigma weight residual 180.00 147.80 32.20 0 5.00e+00 4.00e-02 4.15e+01 ... (remaining 12669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2486 0.078 - 0.155: 606 0.155 - 0.233: 37 0.233 - 0.311: 13 0.311 - 0.388: 2 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CB ILE A 68 " pdb=" CA ILE A 68 " pdb=" CG1 ILE A 68 " pdb=" CG2 ILE A 68 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB VAL E 164 " pdb=" CA VAL E 164 " pdb=" CG1 VAL E 164 " pdb=" CG2 VAL E 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB VAL F 136 " pdb=" CA VAL F 136 " pdb=" CG1 VAL F 136 " pdb=" CG2 VAL F 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 3141 not shown) Planarity restraints: 3684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 26 " -0.054 2.00e-02 2.50e+03 5.27e-02 4.86e+01 pdb=" CG PHE J 26 " 0.119 2.00e-02 2.50e+03 pdb=" CD1 PHE J 26 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE J 26 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE J 26 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE J 26 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE J 26 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 43 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO L 44 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 32 " 0.028 2.00e-02 2.50e+03 2.49e-02 1.55e+01 pdb=" CG TRP G 32 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP G 32 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP G 32 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 32 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 32 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 32 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 32 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP G 32 " 0.005 2.00e-02 2.50e+03 ... (remaining 3681 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 335 2.60 - 3.18: 19507 3.18 - 3.75: 35806 3.75 - 4.33: 52859 4.33 - 4.90: 84199 Nonbonded interactions: 192706 Sorted by model distance: nonbonded pdb=" OH TYR A 138 " pdb=" OE2 GLU B 148 " model vdw 2.027 3.040 nonbonded pdb=" OG1 THR I 187 " pdb=" OD1 ASP I 189 " model vdw 2.033 3.040 nonbonded pdb=" O PRO H 183 " pdb=" NH2 ARG H 194 " model vdw 2.044 3.120 nonbonded pdb=" OE2 GLU C 148 " pdb=" OH TYR D 138 " model vdw 2.083 3.040 nonbonded pdb=" OE2 GLU G 148 " pdb=" OH TYR H 138 " model vdw 2.111 3.040 ... (remaining 192701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'B' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'C' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'D' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'E' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'F' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'G' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'H' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'I' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'J' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'K' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'L' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 48.840 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.011 0.106 21420 Z= 0.692 Angle : 0.955 12.780 29064 Z= 0.513 Chirality : 0.065 0.388 3144 Planarity : 0.006 0.105 3684 Dihedral : 14.251 87.604 7848 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.22 % Favored : 91.67 % Rotamer: Outliers : 0.09 % Allowed : 1.22 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.15), residues: 2556 helix: -1.34 (0.16), residues: 858 sheet: -1.64 (0.27), residues: 353 loop : -1.61 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP G 32 HIS 0.021 0.003 HIS D 78 PHE 0.119 0.004 PHE J 26 TYR 0.027 0.003 TYR A 212 ARG 0.007 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 412 time to evaluate : 2.391 Fit side-chains REVERT: B 45 VAL cc_start: 0.7569 (p) cc_final: 0.7320 (t) REVERT: B 86 LYS cc_start: 0.7995 (tttm) cc_final: 0.7767 (tttp) REVERT: D 108 LYS cc_start: 0.7431 (mptt) cc_final: 0.6900 (mmtp) REVERT: E 88 ASN cc_start: 0.8710 (m110) cc_final: 0.8487 (m-40) REVERT: I 100 ASP cc_start: 0.8129 (t70) cc_final: 0.7762 (OUTLIER) REVERT: I 200 LYS cc_start: 0.7260 (ptpt) cc_final: 0.6879 (ptpt) REVERT: K 148 GLU cc_start: 0.7614 (mm-30) cc_final: 0.6629 (tp30) outliers start: 2 outliers final: 2 residues processed: 413 average time/residue: 1.3501 time to fit residues: 635.0466 Evaluate side-chains 301 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 136 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN C 173 ASN G 193 GLN H 193 GLN I 17 HIS K 29 GLN L 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21420 Z= 0.247 Angle : 0.698 13.061 29064 Z= 0.361 Chirality : 0.051 0.182 3144 Planarity : 0.005 0.093 3684 Dihedral : 6.163 47.592 2749 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.40 % Favored : 94.48 % Rotamer: Outliers : 1.80 % Allowed : 12.34 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.46 (0.16), residues: 2556 helix: -0.13 (0.17), residues: 858 sheet: -1.71 (0.28), residues: 345 loop : -1.29 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 32 HIS 0.007 0.001 HIS D 78 PHE 0.018 0.002 PHE C 210 TYR 0.022 0.002 TYR L 212 ARG 0.006 0.001 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 382 time to evaluate : 2.621 Fit side-chains REVERT: A 63 LEU cc_start: 0.7963 (tt) cc_final: 0.7679 (mp) REVERT: C 7 LYS cc_start: 0.6864 (tppt) cc_final: 0.6487 (tptt) REVERT: C 24 ASP cc_start: 0.7344 (p0) cc_final: 0.6782 (m-30) REVERT: D 4 ILE cc_start: 0.7889 (mm) cc_final: 0.7651 (mm) REVERT: F 7 LYS cc_start: 0.7758 (mmmt) cc_final: 0.7552 (tptp) REVERT: G 49 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7637 (mt-10) REVERT: G 188 VAL cc_start: 0.7840 (t) cc_final: 0.7627 (m) REVERT: H 82 MET cc_start: 0.7761 (mtp) cc_final: 0.7525 (mtp) REVERT: I 100 ASP cc_start: 0.8111 (t70) cc_final: 0.7842 (OUTLIER) REVERT: I 186 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7722 (p) REVERT: I 200 LYS cc_start: 0.7319 (ptpt) cc_final: 0.6872 (ptpt) REVERT: L 49 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7112 (mt-10) REVERT: L 132 ILE cc_start: 0.8071 (mt) cc_final: 0.7829 (mt) outliers start: 40 outliers final: 15 residues processed: 406 average time/residue: 1.2891 time to fit residues: 600.0365 Evaluate side-chains 332 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 317 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN G 173 ASN G 193 GLN H 193 GLN I 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 21420 Z= 0.486 Angle : 0.758 11.579 29064 Z= 0.395 Chirality : 0.055 0.215 3144 Planarity : 0.006 0.102 3684 Dihedral : 6.357 49.026 2749 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.00 % Favored : 92.88 % Rotamer: Outliers : 3.74 % Allowed : 16.04 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.61 (0.16), residues: 2556 helix: -0.26 (0.17), residues: 879 sheet: -1.81 (0.27), residues: 353 loop : -1.38 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 208 HIS 0.009 0.002 HIS D 78 PHE 0.024 0.003 PHE B 33 TYR 0.022 0.002 TYR L 212 ARG 0.006 0.001 ARG H 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 327 time to evaluate : 2.444 Fit side-chains REVERT: A 29 GLN cc_start: 0.7324 (pm20) cc_final: 0.6521 (pt0) REVERT: A 63 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7681 (tt) REVERT: B 56 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7334 (ptm160) REVERT: B 73 ASP cc_start: 0.7427 (m-30) cc_final: 0.7200 (m-30) REVERT: C 24 ASP cc_start: 0.7395 (p0) cc_final: 0.6821 (m-30) REVERT: C 74 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: E 14 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7446 (mtpt) REVERT: F 63 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8231 (tt) REVERT: F 73 ASP cc_start: 0.8203 (m-30) cc_final: 0.7859 (m-30) REVERT: F 87 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: G 49 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7640 (mt-10) REVERT: G 188 VAL cc_start: 0.7969 (t) cc_final: 0.7750 (m) REVERT: H 82 MET cc_start: 0.7784 (mtp) cc_final: 0.7546 (mtp) REVERT: I 200 LYS cc_start: 0.7319 (ptpt) cc_final: 0.6710 (ptpt) REVERT: L 49 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7125 (mt-10) REVERT: L 129 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7681 (tppt) outliers start: 83 outliers final: 44 residues processed: 386 average time/residue: 1.1913 time to fit residues: 530.8273 Evaluate side-chains 356 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 305 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 181 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 230 optimal weight: 0.5980 chunk 243 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 218 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 ASN D 193 GLN G 193 GLN H 193 GLN I 193 GLN L 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21420 Z= 0.217 Angle : 0.644 11.998 29064 Z= 0.330 Chirality : 0.049 0.240 3144 Planarity : 0.005 0.091 3684 Dihedral : 5.893 49.150 2749 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 3.29 % Allowed : 18.29 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.09 (0.16), residues: 2556 helix: 0.50 (0.17), residues: 872 sheet: -1.82 (0.27), residues: 345 loop : -1.22 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 208 HIS 0.005 0.001 HIS B 168 PHE 0.017 0.002 PHE L 33 TYR 0.027 0.002 TYR L 212 ARG 0.003 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 372 time to evaluate : 2.416 Fit side-chains REVERT: B 24 ASP cc_start: 0.3092 (OUTLIER) cc_final: 0.2862 (m-30) REVERT: B 56 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8107 (ptm160) REVERT: B 73 ASP cc_start: 0.7263 (m-30) cc_final: 0.6968 (m-30) REVERT: C 7 LYS cc_start: 0.7225 (ttmt) cc_final: 0.6643 (tptt) REVERT: C 24 ASP cc_start: 0.7350 (p0) cc_final: 0.6787 (m-30) REVERT: D 4 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7658 (mm) REVERT: D 14 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7247 (pttp) REVERT: D 75 VAL cc_start: 0.8818 (t) cc_final: 0.8602 (t) REVERT: D 104 GLU cc_start: 0.7316 (tp30) cc_final: 0.7076 (tp30) REVERT: D 108 LYS cc_start: 0.7200 (mmtp) cc_final: 0.6972 (mmtp) REVERT: D 187 THR cc_start: 0.8389 (m) cc_final: 0.8184 (p) REVERT: F 7 LYS cc_start: 0.7806 (mmmt) cc_final: 0.7556 (tptp) REVERT: F 63 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8066 (tt) REVERT: F 73 ASP cc_start: 0.7896 (m-30) cc_final: 0.7654 (m-30) REVERT: F 87 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: G 49 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7579 (mt-10) REVERT: G 188 VAL cc_start: 0.7929 (t) cc_final: 0.7688 (m) REVERT: H 82 MET cc_start: 0.7712 (mtp) cc_final: 0.7488 (mtp) REVERT: I 178 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7856 (p0) REVERT: I 200 LYS cc_start: 0.7313 (ptpt) cc_final: 0.6999 (pttt) REVERT: J 104 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7000 (mt-10) REVERT: J 192 LYS cc_start: 0.8035 (tmtt) cc_final: 0.7748 (tmmm) REVERT: L 49 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7302 (mt-10) outliers start: 73 outliers final: 40 residues processed: 415 average time/residue: 1.2108 time to fit residues: 581.5067 Evaluate side-chains 362 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 78 HIS Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN E 88 ASN G 173 ASN G 193 GLN H 193 GLN I 193 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21420 Z= 0.323 Angle : 0.676 11.705 29064 Z= 0.347 Chirality : 0.050 0.188 3144 Planarity : 0.005 0.094 3684 Dihedral : 5.919 50.030 2749 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.39 % Rotamer: Outliers : 3.87 % Allowed : 19.91 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.05 (0.16), residues: 2556 helix: 0.54 (0.17), residues: 872 sheet: -1.79 (0.28), residues: 348 loop : -1.21 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 208 HIS 0.005 0.001 HIS L 38 PHE 0.020 0.002 PHE D 33 TYR 0.025 0.002 TYR L 212 ARG 0.003 0.000 ARG H 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 325 time to evaluate : 2.364 Fit side-chains revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8046 (ptm160) REVERT: B 73 ASP cc_start: 0.7404 (m-30) cc_final: 0.7068 (m-30) REVERT: B 74 GLN cc_start: 0.6546 (mm-40) cc_final: 0.5974 (mt0) REVERT: C 7 LYS cc_start: 0.7256 (ttmt) cc_final: 0.6594 (tptt) REVERT: C 24 ASP cc_start: 0.7349 (p0) cc_final: 0.6754 (m-30) REVERT: C 74 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: D 14 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7259 (pttp) REVERT: D 24 ASP cc_start: 0.7233 (p0) cc_final: 0.6440 (m-30) REVERT: E 14 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7400 (mtpt) REVERT: E 87 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7231 (tp30) REVERT: F 63 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8076 (tt) REVERT: F 87 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: G 49 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7634 (mt-10) REVERT: G 188 VAL cc_start: 0.7946 (t) cc_final: 0.7703 (m) REVERT: H 76 PHE cc_start: 0.8659 (t80) cc_final: 0.8376 (t80) REVERT: H 82 MET cc_start: 0.7717 (mtp) cc_final: 0.7505 (mtp) REVERT: H 192 LYS cc_start: 0.7552 (tppt) cc_final: 0.7153 (tptm) REVERT: I 178 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7916 (p0) REVERT: I 200 LYS cc_start: 0.7320 (ptpt) cc_final: 0.7026 (pttt) REVERT: J 104 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7052 (mt-10) REVERT: J 192 LYS cc_start: 0.8057 (tmtt) cc_final: 0.7762 (tmmm) REVERT: L 49 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7178 (mt-10) outliers start: 86 outliers final: 52 residues processed: 380 average time/residue: 1.1897 time to fit residues: 527.8840 Evaluate side-chains 368 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 308 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 GLN Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 181 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 143 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN H 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 21420 Z= 0.344 Angle : 0.687 11.610 29064 Z= 0.352 Chirality : 0.051 0.186 3144 Planarity : 0.005 0.095 3684 Dihedral : 5.938 51.447 2749 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.18 % Favored : 93.70 % Rotamer: Outliers : 4.10 % Allowed : 20.59 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.09 (0.16), residues: 2556 helix: 0.50 (0.17), residues: 872 sheet: -1.80 (0.27), residues: 358 loop : -1.22 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 32 HIS 0.005 0.001 HIS L 38 PHE 0.021 0.002 PHE F 33 TYR 0.024 0.002 TYR I 25 ARG 0.003 0.000 ARG H 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 336 time to evaluate : 2.629 Fit side-chains revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8036 (ptm160) REVERT: B 73 ASP cc_start: 0.7366 (m-30) cc_final: 0.7024 (m-30) REVERT: B 74 GLN cc_start: 0.6563 (mm-40) cc_final: 0.6031 (mt0) REVERT: C 24 ASP cc_start: 0.7316 (p0) cc_final: 0.6802 (m-30) REVERT: C 74 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7125 (mp10) REVERT: D 24 ASP cc_start: 0.7188 (p0) cc_final: 0.6397 (m-30) REVERT: E 14 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7437 (mtpt) REVERT: F 63 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8074 (tt) REVERT: F 87 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: G 49 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7557 (mt-10) REVERT: G 188 VAL cc_start: 0.7966 (t) cc_final: 0.7729 (m) REVERT: G 194 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.7953 (mmt90) REVERT: H 76 PHE cc_start: 0.8683 (t80) cc_final: 0.8395 (t80) REVERT: H 82 MET cc_start: 0.7730 (mtp) cc_final: 0.7509 (mtp) REVERT: H 192 LYS cc_start: 0.7519 (tppt) cc_final: 0.7125 (tptm) REVERT: I 111 MET cc_start: 0.8677 (mtm) cc_final: 0.8466 (mtp) REVERT: I 178 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7932 (p0) REVERT: I 200 LYS cc_start: 0.7327 (ptpt) cc_final: 0.7036 (pttt) REVERT: J 104 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7055 (mt-10) REVERT: J 192 LYS cc_start: 0.8062 (tmtt) cc_final: 0.7767 (tmmm) REVERT: L 49 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7198 (mt-10) REVERT: L 129 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7654 (tppt) REVERT: L 204 GLU cc_start: 0.7080 (pm20) cc_final: 0.6816 (pm20) outliers start: 91 outliers final: 61 residues processed: 395 average time/residue: 0.9463 time to fit residues: 432.6869 Evaluate side-chains 377 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 309 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 207 ASP Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 181 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 242 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 193 GLN H 193 GLN L 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21420 Z= 0.281 Angle : 0.666 11.593 29064 Z= 0.339 Chirality : 0.050 0.188 3144 Planarity : 0.005 0.094 3684 Dihedral : 5.848 52.237 2749 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.90 % Rotamer: Outliers : 3.78 % Allowed : 21.44 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.00 (0.16), residues: 2556 helix: 0.57 (0.17), residues: 886 sheet: -1.78 (0.28), residues: 344 loop : -1.18 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 32 HIS 0.005 0.001 HIS B 168 PHE 0.019 0.002 PHE F 33 TYR 0.031 0.002 TYR L 212 ARG 0.004 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 330 time to evaluate : 2.597 Fit side-chains revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8046 (ptm160) REVERT: B 73 ASP cc_start: 0.7359 (m-30) cc_final: 0.6982 (m-30) REVERT: B 74 GLN cc_start: 0.6500 (mm-40) cc_final: 0.6022 (mt0) REVERT: C 7 LYS cc_start: 0.7252 (ttmt) cc_final: 0.6598 (tptt) REVERT: C 24 ASP cc_start: 0.7261 (p0) cc_final: 0.6736 (m-30) REVERT: C 74 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: D 14 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7226 (pttp) REVERT: D 24 ASP cc_start: 0.7213 (p0) cc_final: 0.6453 (m-30) REVERT: D 49 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7876 (tt0) REVERT: D 75 VAL cc_start: 0.8855 (t) cc_final: 0.8614 (t) REVERT: E 14 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7435 (mtpt) REVERT: E 59 GLN cc_start: 0.8493 (mt0) cc_final: 0.8267 (mt0) REVERT: F 63 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8012 (tt) REVERT: F 87 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: G 49 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7639 (mt-10) REVERT: G 188 VAL cc_start: 0.7906 (t) cc_final: 0.7619 (m) REVERT: G 194 ARG cc_start: 0.8253 (mmt-90) cc_final: 0.7949 (mmt90) REVERT: H 76 PHE cc_start: 0.8655 (t80) cc_final: 0.8348 (t80) REVERT: H 82 MET cc_start: 0.7724 (mtp) cc_final: 0.7493 (mtp) REVERT: H 192 LYS cc_start: 0.7548 (tppt) cc_final: 0.7172 (tptm) REVERT: I 111 MET cc_start: 0.8665 (mtm) cc_final: 0.8336 (mtp) REVERT: I 178 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7883 (p0) REVERT: I 200 LYS cc_start: 0.7259 (ptpt) cc_final: 0.6975 (pttt) REVERT: J 104 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7053 (mt-10) REVERT: J 192 LYS cc_start: 0.8072 (tmtt) cc_final: 0.7767 (tmmm) REVERT: L 49 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7190 (mt-10) REVERT: L 204 GLU cc_start: 0.7120 (pm20) cc_final: 0.6905 (pm20) outliers start: 84 outliers final: 61 residues processed: 384 average time/residue: 1.1356 time to fit residues: 506.0765 Evaluate side-chains 384 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 316 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 78 HIS Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 181 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 0.1980 chunk 165 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 190 optimal weight: 0.0040 chunk 220 optimal weight: 0.7980 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN H 193 GLN L 193 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21420 Z= 0.262 Angle : 0.658 11.530 29064 Z= 0.334 Chirality : 0.049 0.216 3144 Planarity : 0.005 0.092 3684 Dihedral : 5.762 51.896 2749 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.83 % Favored : 94.05 % Rotamer: Outliers : 3.65 % Allowed : 22.21 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -0.91 (0.16), residues: 2556 helix: 0.66 (0.17), residues: 892 sheet: -1.76 (0.28), residues: 339 loop : -1.13 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 81 HIS 0.004 0.001 HIS C 168 PHE 0.018 0.002 PHE F 33 TYR 0.030 0.002 TYR L 212 ARG 0.003 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 327 time to evaluate : 2.440 Fit side-chains revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.8001 (ptm160) REVERT: B 73 ASP cc_start: 0.7315 (m-30) cc_final: 0.6956 (m-30) REVERT: B 192 LYS cc_start: 0.7870 (mmtp) cc_final: 0.7446 (mttp) REVERT: C 7 LYS cc_start: 0.7236 (ttmt) cc_final: 0.6564 (tptt) REVERT: C 74 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7073 (mp10) REVERT: D 14 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7308 (ttpm) REVERT: D 24 ASP cc_start: 0.7152 (p0) cc_final: 0.6412 (m-30) REVERT: D 49 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7856 (tt0) REVERT: D 75 VAL cc_start: 0.8847 (t) cc_final: 0.8629 (t) REVERT: E 14 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7426 (mtpt) REVERT: F 63 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8004 (tt) REVERT: F 87 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: G 49 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7606 (mt-10) REVERT: G 188 VAL cc_start: 0.7820 (t) cc_final: 0.7552 (m) REVERT: H 1 MET cc_start: 0.6160 (tpt) cc_final: 0.5728 (tpp) REVERT: H 76 PHE cc_start: 0.8617 (t80) cc_final: 0.8387 (t80) REVERT: H 82 MET cc_start: 0.7686 (mtp) cc_final: 0.7459 (mtp) REVERT: H 192 LYS cc_start: 0.7529 (tppt) cc_final: 0.7138 (tptm) REVERT: I 178 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7855 (p0) REVERT: I 200 LYS cc_start: 0.7238 (ptpt) cc_final: 0.6976 (pttt) REVERT: J 104 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7003 (mt-10) REVERT: J 192 LYS cc_start: 0.8047 (tmtt) cc_final: 0.7739 (tmmm) REVERT: L 49 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7161 (mt-10) REVERT: L 112 ILE cc_start: 0.3188 (OUTLIER) cc_final: 0.2985 (tp) outliers start: 81 outliers final: 57 residues processed: 382 average time/residue: 1.1345 time to fit residues: 503.7666 Evaluate side-chains 371 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 306 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 4.9990 chunk 212 optimal weight: 0.0000 chunk 226 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 98 optimal weight: 0.0170 chunk 177 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 204 optimal weight: 0.5980 chunk 214 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 overall best weight: 0.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 193 GLN H 193 GLN K 54 GLN L 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21420 Z= 0.172 Angle : 0.629 12.193 29064 Z= 0.317 Chirality : 0.048 0.212 3144 Planarity : 0.004 0.087 3684 Dihedral : 5.477 49.380 2749 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 3.06 % Allowed : 23.42 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -0.60 (0.17), residues: 2556 helix: 1.12 (0.18), residues: 880 sheet: -1.78 (0.28), residues: 351 loop : -1.03 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 81 HIS 0.003 0.001 HIS B 168 PHE 0.014 0.001 PHE L 33 TYR 0.029 0.002 TYR L 212 ARG 0.004 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 345 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.7117 (m-30) cc_final: 0.6795 (m-30) REVERT: B 192 LYS cc_start: 0.7764 (mmtp) cc_final: 0.7420 (mttp) REVERT: C 24 ASP cc_start: 0.7205 (p0) cc_final: 0.6574 (m-30) REVERT: C 74 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: D 1 MET cc_start: 0.4119 (mmm) cc_final: 0.3871 (ttp) REVERT: D 14 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7199 (pttp) REVERT: D 24 ASP cc_start: 0.7056 (p0) cc_final: 0.6338 (m-30) REVERT: D 75 VAL cc_start: 0.8688 (t) cc_final: 0.8416 (t) REVERT: F 63 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7928 (tt) REVERT: F 87 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: F 169 LYS cc_start: 0.8774 (tttp) cc_final: 0.8547 (tttp) REVERT: G 49 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7600 (mt-10) REVERT: H 192 LYS cc_start: 0.7470 (tppt) cc_final: 0.7067 (tptm) REVERT: I 178 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7640 (p0) REVERT: J 1 MET cc_start: 0.5947 (tpp) cc_final: 0.5346 (tpt) REVERT: J 86 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7842 (tptt) REVERT: J 104 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6913 (mt-10) REVERT: J 192 LYS cc_start: 0.8018 (tmtt) cc_final: 0.7710 (tmmm) REVERT: L 49 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7023 (mt-10) REVERT: L 112 ILE cc_start: 0.3096 (OUTLIER) cc_final: 0.2889 (tp) REVERT: L 129 LYS cc_start: 0.8035 (mppt) cc_final: 0.7783 (mptp) outliers start: 68 outliers final: 45 residues processed: 394 average time/residue: 1.1919 time to fit residues: 540.6805 Evaluate side-chains 357 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 78 HIS Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 251 optimal weight: 0.0040 chunk 231 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN H 193 GLN L 193 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21420 Z= 0.207 Angle : 0.646 12.034 29064 Z= 0.325 Chirality : 0.049 0.202 3144 Planarity : 0.005 0.090 3684 Dihedral : 5.467 49.992 2749 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.32 % Favored : 94.56 % Rotamer: Outliers : 2.79 % Allowed : 24.50 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -0.54 (0.17), residues: 2556 helix: 1.15 (0.18), residues: 880 sheet: -1.72 (0.28), residues: 351 loop : -0.99 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 81 HIS 0.004 0.001 HIS B 168 PHE 0.017 0.001 PHE J 33 TYR 0.029 0.002 TYR L 212 ARG 0.009 0.000 ARG F 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 329 time to evaluate : 2.453 Fit side-chains revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7269 (ptm160) REVERT: B 73 ASP cc_start: 0.7154 (m-30) cc_final: 0.6804 (m-30) REVERT: B 192 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7519 (mttp) REVERT: C 74 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7053 (mp10) REVERT: D 14 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7228 (pttp) REVERT: D 24 ASP cc_start: 0.7076 (p0) cc_final: 0.6358 (m-30) REVERT: D 49 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7833 (tt0) REVERT: D 75 VAL cc_start: 0.8701 (t) cc_final: 0.8437 (t) REVERT: F 87 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: F 169 LYS cc_start: 0.8802 (tttp) cc_final: 0.8557 (tttp) REVERT: H 192 LYS cc_start: 0.7461 (tppt) cc_final: 0.7060 (tptm) REVERT: I 129 LYS cc_start: 0.8424 (mppt) cc_final: 0.7936 (mmtt) REVERT: I 178 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7667 (p0) REVERT: J 1 MET cc_start: 0.5972 (tpp) cc_final: 0.5381 (tpt) REVERT: J 86 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7828 (tptt) REVERT: J 87 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: J 104 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6916 (mt-10) REVERT: J 192 LYS cc_start: 0.7996 (tmtt) cc_final: 0.7689 (tmmm) REVERT: L 49 GLU cc_start: 0.7859 (mt-10) cc_final: 0.6909 (mt-10) REVERT: L 112 ILE cc_start: 0.3208 (OUTLIER) cc_final: 0.3005 (tp) REVERT: L 129 LYS cc_start: 0.8050 (mppt) cc_final: 0.7813 (mptp) outliers start: 62 outliers final: 48 residues processed: 373 average time/residue: 1.1421 time to fit residues: 496.1512 Evaluate side-chains 357 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 302 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 78 HIS Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 205 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN H 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.176071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144673 restraints weight = 23565.878| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.14 r_work: 0.3445 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21420 Z= 0.223 Angle : 0.649 11.741 29064 Z= 0.327 Chirality : 0.049 0.195 3144 Planarity : 0.004 0.090 3684 Dihedral : 5.484 51.047 2749 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.52 % Rotamer: Outliers : 3.02 % Allowed : 24.37 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -0.55 (0.17), residues: 2556 helix: 1.11 (0.18), residues: 880 sheet: -1.72 (0.28), residues: 351 loop : -0.97 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 81 HIS 0.004 0.001 HIS B 168 PHE 0.017 0.001 PHE J 33 TYR 0.028 0.002 TYR L 212 ARG 0.007 0.000 ARG F 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8294.84 seconds wall clock time: 241 minutes 12.91 seconds (14472.91 seconds total)