Starting phenix.real_space_refine on Sun Sep 13 14:46:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5o4u_3746/09_2026/5o4u_3746.cif Found real_map, /net/cci-nas-00/data/ceres_data/5o4u_3746/09_2026/5o4u_3746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5o4u_3746/09_2026/5o4u_3746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5o4u_3746/09_2026/5o4u_3746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5o4u_3746/09_2026/5o4u_3746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5o4u_3746/09_2026/5o4u_3746.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 16 5.16 5 C 15600 2.51 5 N 4064 2.21 5 O 4848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24528 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "B" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "C" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "D" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "E" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "F" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "G" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "H" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "I" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "J" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "K" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "L" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "M" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "N" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "O" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "P" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Time building chain proxies: 5.86, per 1000 atoms: 0.24 Number of scatterers: 24528 At special positions: 0 Unit cell: (112, 114.24, 198.24, 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 16 16.00 O 4848 8.00 N 4064 7.00 C 15600 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 1.4 seconds 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5952 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 55 sheets defined 23.8% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 6 through 53 removed outlier: 3.734A pdb=" N GLY A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 11 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 12 " --> pdb=" O GLY A 8 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 53 " --> pdb=" O GLN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.770A pdb=" N TRP A 127 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.940A pdb=" N VAL B 19 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 53 removed outlier: 3.656A pdb=" N TYR B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 53 " --> pdb=" O GLN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'C' and resid 7 through 53 removed outlier: 3.808A pdb=" N THR C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 20 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 42 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR C 48 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 53 " --> pdb=" O GLN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.771A pdb=" N THR C 92 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 53 removed outlier: 4.095A pdb=" N LEU D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 20 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 37 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.834A pdb=" N TRP D 127 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN D 128 " --> pdb=" O THR D 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 124 through 128' Processing helix chain 'E' and resid 7 through 53 removed outlier: 3.586A pdb=" N THR E 11 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 53 " --> pdb=" O GLN E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.674A pdb=" N TRP E 127 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN E 128 " --> pdb=" O THR E 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 128' Processing helix chain 'F' and resid 9 through 25 removed outlier: 3.682A pdb=" N VAL F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 38 removed outlier: 3.937A pdb=" N GLN F 38 " --> pdb=" O GLY F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 53 removed outlier: 3.942A pdb=" N THR F 47 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR F 48 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN F 49 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL F 51 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER F 53 " --> pdb=" O GLN F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.592A pdb=" N TRP F 127 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN F 128 " --> pdb=" O THR F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 124 through 128' Processing helix chain 'G' and resid 7 through 25 removed outlier: 3.616A pdb=" N LEU G 20 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 52 removed outlier: 3.634A pdb=" N LEU G 36 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN G 37 " --> pdb=" O SER G 33 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA G 42 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG G 45 " --> pdb=" O GLN G 41 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 128 removed outlier: 3.684A pdb=" N TRP G 127 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN G 128 " --> pdb=" O THR G 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 128' Processing helix chain 'H' and resid 9 through 25 removed outlier: 3.759A pdb=" N VAL H 14 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE H 15 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU H 20 " --> pdb=" O ILE H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 53 removed outlier: 3.583A pdb=" N TYR H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU H 36 " --> pdb=" O THR H 32 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA H 42 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR H 47 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL H 51 " --> pdb=" O THR H 47 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER H 53 " --> pdb=" O GLN H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 128 removed outlier: 3.819A pdb=" N TRP H 127 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN H 128 " --> pdb=" O THR H 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 124 through 128' Processing helix chain 'I' and resid 7 through 45 removed outlier: 3.560A pdb=" N THR I 11 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU I 12 " --> pdb=" O GLY I 8 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE I 13 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL I 19 " --> pdb=" O PHE I 15 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU I 20 " --> pdb=" O ILE I 16 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 29 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 53 removed outlier: 4.223A pdb=" N VAL I 51 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 128 removed outlier: 3.705A pdb=" N TRP I 127 " --> pdb=" O SER I 124 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN I 128 " --> pdb=" O THR I 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 124 through 128' Processing helix chain 'J' and resid 7 through 27 removed outlier: 3.788A pdb=" N ILE J 16 " --> pdb=" O LEU J 12 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA J 17 " --> pdb=" O ILE J 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET J 18 " --> pdb=" O VAL J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 53 removed outlier: 3.510A pdb=" N TYR J 35 " --> pdb=" O GLN J 31 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN J 37 " --> pdb=" O SER J 33 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR J 43 " --> pdb=" O LYS J 39 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR J 48 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER J 53 " --> pdb=" O GLN J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 128 removed outlier: 3.929A pdb=" N TRP J 127 " --> pdb=" O SER J 124 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN J 128 " --> pdb=" O THR J 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 128' Processing helix chain 'K' and resid 9 through 53 removed outlier: 3.569A pdb=" N ILE K 13 " --> pdb=" O ILE K 9 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE K 15 " --> pdb=" O THR K 11 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 41 removed outlier: 3.583A pdb=" N LEU L 20 " --> pdb=" O ILE L 16 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 53 removed outlier: 3.570A pdb=" N ARG L 45 " --> pdb=" O GLN L 41 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU L 46 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR L 47 " --> pdb=" O THR L 43 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR L 48 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL L 51 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER L 53 " --> pdb=" O GLN L 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 28 removed outlier: 3.624A pdb=" N VAL M 24 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL M 28 " --> pdb=" O VAL M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 53 removed outlier: 3.576A pdb=" N LEU M 36 " --> pdb=" O THR M 32 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN M 37 " --> pdb=" O SER M 33 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN M 38 " --> pdb=" O GLY M 34 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA M 42 " --> pdb=" O GLN M 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG M 45 " --> pdb=" O GLN M 41 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR M 48 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL M 51 " --> pdb=" O THR M 47 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER M 53 " --> pdb=" O GLN M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 128 removed outlier: 3.839A pdb=" N TRP M 127 " --> pdb=" O SER M 124 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN M 128 " --> pdb=" O THR M 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 124 through 128' Processing helix chain 'N' and resid 7 through 30 removed outlier: 3.702A pdb=" N THR N 11 " --> pdb=" O VAL N 7 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU N 12 " --> pdb=" O GLY N 8 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE N 13 " --> pdb=" O ILE N 9 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL N 28 " --> pdb=" O VAL N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 53 removed outlier: 4.038A pdb=" N GLN N 37 " --> pdb=" O SER N 33 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN N 38 " --> pdb=" O GLY N 34 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS N 39 " --> pdb=" O TYR N 35 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA N 42 " --> pdb=" O GLN N 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR N 43 " --> pdb=" O LYS N 39 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG N 45 " --> pdb=" O GLN N 41 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR N 48 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL N 51 " --> pdb=" O THR N 47 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 28 removed outlier: 4.557A pdb=" N LEU O 12 " --> pdb=" O GLY O 8 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL O 28 " --> pdb=" O VAL O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 50 removed outlier: 3.724A pdb=" N SER O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA O 42 " --> pdb=" O GLN O 38 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR O 43 " --> pdb=" O LYS O 39 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR O 47 " --> pdb=" O THR O 43 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR O 48 " --> pdb=" O GLY O 44 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN O 49 " --> pdb=" O ARG O 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 53 removed outlier: 3.501A pdb=" N ILE P 16 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA P 42 " --> pdb=" O GLN P 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR P 48 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL P 51 " --> pdb=" O THR P 47 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER P 53 " --> pdb=" O GLN P 49 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 removed outlier: 3.540A pdb=" N SER A 79 " --> pdb=" O LYS A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 removed outlier: 7.188A pdb=" N LYS A 106 " --> pdb=" O PHE A 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.614A pdb=" N ASP A 147 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 61 removed outlier: 5.272A pdb=" N VAL B 57 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER B 79 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER B 59 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR B 77 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS B 164 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASN B 133 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS B 106 " --> pdb=" O PHE B 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 61 removed outlier: 5.272A pdb=" N VAL B 57 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER B 79 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER B 59 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR B 77 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 158 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 139 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.634A pdb=" N ILE B 87 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 150 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 55 through 57 removed outlier: 3.656A pdb=" N SER C 79 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 158 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 139 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS C 164 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C 133 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LYS C 106 " --> pdb=" O PHE C 134 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ILE C 136 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.673A pdb=" N ARG C 93 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 182 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 196 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.510A pdb=" N ASP C 147 " --> pdb=" O TYR C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 55 through 61 removed outlier: 3.543A pdb=" N SER D 79 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR D 77 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL D 60 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA D 75 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 158 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 139 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.996A pdb=" N ILE D 87 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 92 through 96 Processing sheet with id=AB6, first strand: chain 'D' and resid 106 through 107 removed outlier: 6.985A pdb=" N LYS D 106 " --> pdb=" O PHE D 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 55 through 61 removed outlier: 3.941A pdb=" N TYR E 77 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL E 60 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA E 75 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LYS E 164 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN E 133 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS E 106 " --> pdb=" O PHE E 134 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N ILE E 136 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.903A pdb=" N ILE E 87 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 153 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 150 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP E 147 " --> pdb=" O TYR E 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 93 through 96 removed outlier: 3.569A pdb=" N ARG E 93 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 55 through 61 removed outlier: 5.298A pdb=" N VAL F 57 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N SER F 79 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER F 59 " --> pdb=" O TYR F 77 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR F 77 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 87 through 88 removed outlier: 3.710A pdb=" N TYR F 150 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP F 147 " --> pdb=" O TYR F 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 93 through 97 Processing sheet with id=AC4, first strand: chain 'F' and resid 106 through 107 removed outlier: 7.010A pdb=" N LYS F 106 " --> pdb=" O PHE F 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 55 through 61 removed outlier: 5.243A pdb=" N VAL G 57 " --> pdb=" O SER G 79 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER G 79 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER G 59 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR G 77 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS G 164 " --> pdb=" O ASN G 133 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN G 133 " --> pdb=" O LYS G 164 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE G 134 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LYS G 106 " --> pdb=" O PHE G 134 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE G 136 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG G 93 " --> pdb=" O ILE G 187 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 187 " --> pdb=" O ARG G 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 87 through 88 removed outlier: 3.520A pdb=" N ILE G 87 " --> pdb=" O LEU G 153 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 55 through 57 removed outlier: 7.310A pdb=" N LYS H 106 " --> pdb=" O PHE H 134 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N ILE H 136 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 87 through 88 removed outlier: 3.532A pdb=" N ILE H 87 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP H 147 " --> pdb=" O TYR H 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 93 through 96 removed outlier: 3.535A pdb=" N ARG H 93 " --> pdb=" O ILE H 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 55 through 57 removed outlier: 3.525A pdb=" N SER I 79 " --> pdb=" O LYS I 56 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 87 through 88 removed outlier: 3.585A pdb=" N ILE I 87 " --> pdb=" O LEU I 153 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 93 through 96 removed outlier: 3.801A pdb=" N ARG I 93 " --> pdb=" O ILE I 187 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE I 187 " --> pdb=" O ARG I 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 55 through 61 removed outlier: 3.551A pdb=" N LEU J 58 " --> pdb=" O TYR J 77 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR J 77 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL J 60 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA J 75 " --> pdb=" O VAL J 60 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AD6, first strand: chain 'J' and resid 133 through 134 removed outlier: 7.522A pdb=" N PHE J 134 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LYS J 106 " --> pdb=" O PHE J 134 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL J 94 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG J 93 " --> pdb=" O ILE J 187 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE J 187 " --> pdb=" O ARG J 93 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE J 182 " --> pdb=" O PHE J 198 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 55 through 61 removed outlier: 3.766A pdb=" N LEU K 58 " --> pdb=" O TYR K 77 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR K 77 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL K 60 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA K 75 " --> pdb=" O VAL K 60 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 87 through 88 removed outlier: 3.667A pdb=" N ASP K 147 " --> pdb=" O TYR K 150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 93 through 96 removed outlier: 3.744A pdb=" N ILE K 187 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 106 through 107 removed outlier: 6.962A pdb=" N LYS K 106 " --> pdb=" O PHE K 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'L' and resid 55 through 57 removed outlier: 4.912A pdb=" N LYS L 164 " --> pdb=" O ASN L 133 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN L 133 " --> pdb=" O LYS L 164 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS L 106 " --> pdb=" O PHE L 134 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ILE L 136 " --> pdb=" O LYS L 106 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 87 through 88 removed outlier: 3.739A pdb=" N ILE L 87 " --> pdb=" O LEU L 153 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 93 through 96 removed outlier: 3.575A pdb=" N ARG L 93 " --> pdb=" O ILE L 187 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE L 187 " --> pdb=" O ARG L 93 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 55 through 57 removed outlier: 3.542A pdb=" N SER M 79 " --> pdb=" O LYS M 56 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 87 through 88 removed outlier: 4.015A pdb=" N ILE M 87 " --> pdb=" O LEU M 153 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 93 through 96 removed outlier: 3.816A pdb=" N ARG M 93 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE M 187 " --> pdb=" O ARG M 93 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 55 through 57 Processing sheet with id=AE9, first strand: chain 'N' and resid 87 through 88 removed outlier: 3.866A pdb=" N ILE N 87 " --> pdb=" O LEU N 153 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 93 through 96 removed outlier: 3.708A pdb=" N ARG N 93 " --> pdb=" O ILE N 187 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 106 through 107 removed outlier: 7.156A pdb=" N LYS N 106 " --> pdb=" O PHE N 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'O' and resid 55 through 61 removed outlier: 5.117A pdb=" N VAL O 57 " --> pdb=" O SER O 79 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER O 79 " --> pdb=" O VAL O 57 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER O 59 " --> pdb=" O TYR O 77 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR O 77 " --> pdb=" O SER O 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE O 158 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU O 139 " --> pdb=" O ILE O 158 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 93 through 96 removed outlier: 3.513A pdb=" N ARG O 93 " --> pdb=" O ILE O 187 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE O 187 " --> pdb=" O ARG O 93 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 106 through 107 removed outlier: 7.113A pdb=" N LYS O 106 " --> pdb=" O PHE O 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'O' and resid 146 through 147 removed outlier: 3.582A pdb=" N ASP O 147 " --> pdb=" O TYR O 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 55 through 56 Processing sheet with id=AF8, first strand: chain 'P' and resid 87 through 88 removed outlier: 3.606A pdb=" N ILE P 87 " --> pdb=" O LEU P 153 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 93 through 96 removed outlier: 3.683A pdb=" N ARG P 93 " --> pdb=" O ILE P 187 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 106 through 107 removed outlier: 6.888A pdb=" N LYS P 106 " --> pdb=" O PHE P 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 801 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6332 1.33 - 1.45: 4024 1.45 - 1.57: 14492 1.57 - 1.69: 0 1.69 - 1.80: 32 Bond restraints: 24880 Sorted by residual: bond pdb=" N VAL L 7 " pdb=" CA VAL L 7 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.22e-02 6.72e+03 6.73e+00 bond pdb=" CG1 ILE D 182 " pdb=" CD1 ILE D 182 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.52e+00 bond pdb=" CA VAL J 7 " pdb=" C VAL J 7 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.27e-02 6.20e+03 6.17e+00 bond pdb=" N VAL J 7 " pdb=" CA VAL J 7 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.19e-02 7.06e+03 6.03e+00 bond pdb=" CA VAL L 7 " pdb=" C VAL L 7 " ideal model delta sigma weight residual 1.526 1.557 -0.031 1.32e-02 5.74e+03 5.35e+00 ... (remaining 24875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 32860 3.07 - 6.13: 900 6.13 - 9.20: 115 9.20 - 12.27: 27 12.27 - 15.33: 2 Bond angle restraints: 33904 Sorted by residual: angle pdb=" N VAL J 7 " pdb=" CA VAL J 7 " pdb=" C VAL J 7 " ideal model delta sigma weight residual 110.62 125.95 -15.33 1.02e+00 9.61e-01 2.26e+02 angle pdb=" N VAL G 7 " pdb=" CA VAL G 7 " pdb=" C VAL G 7 " ideal model delta sigma weight residual 110.62 121.27 -10.65 1.02e+00 9.61e-01 1.09e+02 angle pdb=" N VAL M 7 " pdb=" CA VAL M 7 " pdb=" C VAL M 7 " ideal model delta sigma weight residual 110.62 119.37 -8.75 1.02e+00 9.61e-01 7.37e+01 angle pdb=" N VAL B 7 " pdb=" CA VAL B 7 " pdb=" C VAL B 7 " ideal model delta sigma weight residual 113.43 106.79 6.64 1.09e+00 8.42e-01 3.71e+01 angle pdb=" N SER H 40 " pdb=" CA SER H 40 " pdb=" C SER H 40 " ideal model delta sigma weight residual 111.28 117.34 -6.06 1.09e+00 8.42e-01 3.09e+01 ... (remaining 33899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.93: 13346 13.93 - 27.86: 1099 27.86 - 41.78: 272 41.78 - 55.71: 50 55.71 - 69.64: 1 Dihedral angle restraints: 14768 sinusoidal: 5408 harmonic: 9360 Sorted by residual: dihedral pdb=" CA VAL D 208 " pdb=" C VAL D 208 " pdb=" N ILE D 209 " pdb=" CA ILE D 209 " ideal model delta harmonic sigma weight residual -180.00 -146.49 -33.51 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" CA VAL G 208 " pdb=" C VAL G 208 " pdb=" N ILE G 209 " pdb=" CA ILE G 209 " ideal model delta harmonic sigma weight residual 180.00 -148.49 -31.51 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" CA GLU L 207 " pdb=" C GLU L 207 " pdb=" N VAL L 208 " pdb=" CA VAL L 208 " ideal model delta harmonic sigma weight residual -180.00 -148.67 -31.33 0 5.00e+00 4.00e-02 3.93e+01 ... (remaining 14765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3649 0.103 - 0.206: 451 0.206 - 0.309: 71 0.309 - 0.412: 20 0.412 - 0.515: 17 Chirality restraints: 4208 Sorted by residual: chirality pdb=" CB ILE B 182 " pdb=" CA ILE B 182 " pdb=" CG1 ILE B 182 " pdb=" CG2 ILE B 182 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" CB ILE E 182 " pdb=" CA ILE E 182 " pdb=" CG1 ILE E 182 " pdb=" CG2 ILE E 182 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CB ILE M 182 " pdb=" CA ILE M 182 " pdb=" CG1 ILE M 182 " pdb=" CG2 ILE M 182 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.67e+00 ... (remaining 4205 not shown) Planarity restraints: 4320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 200 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO C 201 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 22 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C ALA D 22 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA D 22 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA D 23 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR J 200 " 0.052 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO J 201 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO J 201 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO J 201 " 0.042 5.00e-02 4.00e+02 ... (remaining 4317 not shown) Histogram of nonbonded interaction distances: 0.83 - 1.64: 3 1.64 - 2.46: 153 2.46 - 3.27: 27190 3.27 - 4.09: 59774 4.09 - 4.90: 105792 Warning: very small nonbonded interaction distances. Nonbonded interactions: 192912 Sorted by model distance: nonbonded pdb=" O GLY K 34 " pdb=" OE1 GLN K 37 " model vdw 0.830 3.040 nonbonded pdb=" O GLY K 34 " pdb=" CD GLN K 37 " model vdw 1.291 3.270 nonbonded pdb=" C GLY K 34 " pdb=" CD GLN K 37 " model vdw 1.515 2.800 nonbonded pdb=" C GLY K 34 " pdb=" OE1 GLN K 37 " model vdw 1.668 3.270 nonbonded pdb=" O GLY K 34 " pdb=" NE2 GLN K 37 " model vdw 1.888 2.496 ... (remaining 192907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.970 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.110 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:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 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 : 0.009 0.844 24884 Z= 0.706 Angle : 1.258 15.334 33904 Z= 0.723 Chirality : 0.080 0.515 4208 Planarity : 0.008 0.102 4320 Dihedral : 11.284 69.640 8816 Min Nonbonded Distance : 0.830 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.26 % Favored : 82.74 % Rotamer: Outliers : 1.75 % Allowed : 6.55 % Favored : 91.70 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.12), residues: 3280 helix: -1.82 (0.20), residues: 592 sheet: -3.91 (0.14), residues: 752 loop : -3.29 (0.12), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 93 TYR 0.030 0.003 TYR D 112 PHE 0.033 0.005 PHE E 121 TRP 0.032 0.007 TRP J 127 HIS 0.010 0.003 HIS F 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.32 (24880) covalent geometry : angle 1.25812 / 0.72 (33904) hydrogen bonds : bond 0.28045 / 18.39 ( 793) hydrogen bonds : angle 10.10555 / 6.93 ( 2244) Misc. bond : bond 0.49480 / 24.27 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 1105 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8123 (p) cc_final: 0.7599 (m) REVERT: A 105 LEU cc_start: 0.9266 (mm) cc_final: 0.8878 (mm) REVERT: A 110 THR cc_start: 0.7066 (p) cc_final: 0.6724 (t) REVERT: A 155 LYS cc_start: 0.7359 (ptpt) cc_final: 0.7027 (tptt) REVERT: A 200 THR cc_start: 0.8227 (m) cc_final: 0.7741 (p) REVERT: B 49 GLN cc_start: 0.6462 (mt0) cc_final: 0.6069 (mm-40) REVERT: B 204 TYR cc_start: 0.6839 (p90) cc_final: 0.6583 (p90) REVERT: C 46 GLU cc_start: 0.6335 (mt-10) cc_final: 0.6121 (mt-10) REVERT: C 60 VAL cc_start: 0.9124 (t) cc_final: 0.8861 (m) REVERT: C 150 TYR cc_start: 0.7925 (m-80) cc_final: 0.7579 (m-10) REVERT: D 31 GLN cc_start: 0.6084 (tt0) cc_final: 0.5630 (tt0) REVERT: D 105 LEU cc_start: 0.8275 (mm) cc_final: 0.7994 (mm) REVERT: D 177 PRO cc_start: 0.9000 (Cg_endo) cc_final: 0.8761 (Cg_exo) REVERT: D 200 THR cc_start: 0.8534 (m) cc_final: 0.7869 (p) REVERT: E 105 LEU cc_start: 0.8020 (mm) cc_final: 0.7498 (mm) REVERT: E 110 THR cc_start: 0.8074 (p) cc_final: 0.7419 (t) REVERT: E 150 TYR cc_start: 0.7214 (m-80) cc_final: 0.6884 (m-80) REVERT: E 176 ILE cc_start: 0.8290 (pt) cc_final: 0.7787 (mt) REVERT: E 185 LYS cc_start: 0.8142 (ptmt) cc_final: 0.7839 (pttp) REVERT: E 200 THR cc_start: 0.8534 (m) cc_final: 0.7857 (p) REVERT: F 112 TYR cc_start: 0.7063 (m-80) cc_final: 0.6824 (m-10) REVERT: G 158 ILE cc_start: 0.8944 (mt) cc_final: 0.8665 (mm) REVERT: H 55 ILE cc_start: 0.8671 (mt) cc_final: 0.8406 (mm) REVERT: H 93 ARG cc_start: 0.7587 (mmt-90) cc_final: 0.5985 (mtt180) REVERT: H 139 LEU cc_start: 0.8454 (pp) cc_final: 0.8225 (pp) REVERT: H 140 GLN cc_start: 0.7261 (tt0) cc_final: 0.7059 (tt0) REVERT: H 158 ILE cc_start: 0.8283 (mt) cc_final: 0.7916 (tt) REVERT: H 185 LYS cc_start: 0.8504 (ptmt) cc_final: 0.8150 (pttm) REVERT: I 64 THR cc_start: 0.6747 (t) cc_final: 0.6510 (t) REVERT: I 66 SER cc_start: 0.7573 (m) cc_final: 0.6807 (p) REVERT: I 110 THR cc_start: 0.6836 (p) cc_final: 0.6565 (t) REVERT: I 158 ILE cc_start: 0.8719 (mt) cc_final: 0.8114 (tp) REVERT: I 200 THR cc_start: 0.8416 (m) cc_final: 0.8169 (t) REVERT: I 204 TYR cc_start: 0.6428 (p90) cc_final: 0.5979 (p90) REVERT: J 16 ILE cc_start: 0.9194 (mt) cc_final: 0.8975 (mt) REVERT: J 18 MET cc_start: 0.5331 (ttt) cc_final: 0.4563 (ptp) REVERT: J 35 TYR cc_start: 0.6049 (t80) cc_final: 0.5546 (t80) REVERT: J 56 LYS cc_start: 0.7897 (pttp) cc_final: 0.7664 (ptpp) REVERT: J 202 SER cc_start: 0.7610 (t) cc_final: 0.7364 (m) REVERT: K 56 LYS cc_start: 0.8527 (pttp) cc_final: 0.8269 (pttm) REVERT: K 210 GLU cc_start: 0.8559 (pm20) cc_final: 0.8019 (pm20) REVERT: L 35 TYR cc_start: 0.6832 (t80) cc_final: 0.6044 (t80) REVERT: L 36 LEU cc_start: 0.7503 (mt) cc_final: 0.6947 (mt) REVERT: L 56 LYS cc_start: 0.8238 (pttp) cc_final: 0.7962 (pttm) REVERT: L 183 THR cc_start: 0.8155 (m) cc_final: 0.7787 (p) REVERT: L 202 SER cc_start: 0.5830 (p) cc_final: 0.5166 (p) REVERT: M 73 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7883 (mtmm) REVERT: M 92 THR cc_start: 0.8426 (m) cc_final: 0.8195 (m) REVERT: M 155 LYS cc_start: 0.6971 (ptpt) cc_final: 0.6742 (ptmt) REVERT: M 179 ARG cc_start: 0.6830 (ttp-110) cc_final: 0.6361 (ptp90) REVERT: M 183 THR cc_start: 0.8358 (m) cc_final: 0.8037 (m) REVERT: M 200 THR cc_start: 0.7970 (m) cc_final: 0.7690 (p) REVERT: N 31 GLN cc_start: 0.6008 (tt0) cc_final: 0.5779 (tt0) REVERT: N 55 ILE cc_start: 0.8410 (mt) cc_final: 0.8074 (mm) REVERT: N 73 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7708 (mtmm) REVERT: N 155 LYS cc_start: 0.6786 (ptpt) cc_final: 0.5999 (tmtt) REVERT: O 9 ILE cc_start: 0.5772 (mp) cc_final: 0.5477 (mp) REVERT: O 160 VAL cc_start: 0.8576 (t) cc_final: 0.8252 (t) REVERT: O 199 THR cc_start: 0.7726 (p) cc_final: 0.7450 (t) REVERT: P 18 MET cc_start: 0.5363 (ttt) cc_final: 0.4553 (ttm) REVERT: P 66 SER cc_start: 0.7410 (m) cc_final: 0.6687 (t) REVERT: P 140 GLN cc_start: 0.6616 (tt0) cc_final: 0.5798 (mm110) REVERT: P 172 PHE cc_start: 0.7052 (m-10) cc_final: 0.6148 (m-80) outliers start: 47 outliers final: 25 residues processed: 1126 average time/residue: 0.1469 time to fit residues: 268.3624 Evaluate side-chains 856 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 831 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 133 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN C 140 GLN D 41 GLN D 133 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 ASN E 113 HIS E 133 ASN ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN H 133 ASN ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN I 102 GLN I 113 HIS I 140 GLN J 31 GLN J 41 GLN J 144 ASN K 81 ASN K 91 ASN K 140 GLN K 149 ASN L 49 GLN L 91 ASN L 140 GLN M 31 GLN M 131 ASN M 133 ASN M 149 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 91 ASN N 113 HIS N 149 ASN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 GLN P 149 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.174966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.162621 restraints weight = 33159.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.165653 restraints weight = 20383.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.167665 restraints weight = 13529.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.169035 restraints weight = 9531.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.169860 restraints weight = 7068.725| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24884 Z= 0.216 Angle : 0.807 9.631 33904 Z= 0.431 Chirality : 0.056 0.384 4208 Planarity : 0.007 0.076 4320 Dihedral : 7.727 28.880 3456 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.49 % Favored : 83.51 % Rotamer: Outliers : 0.37 % Allowed : 7.40 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.13), residues: 3280 helix: -0.92 (0.18), residues: 704 sheet: -3.18 (0.17), residues: 576 loop : -3.46 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 179 TYR 0.015 0.002 TYR M 70 PHE 0.028 0.003 PHE C 198 TRP 0.022 0.005 TRP J 127 HIS 0.008 0.002 HIS F 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (24880) covalent geometry : angle 0.80672 / 0.43 (33904) hydrogen bonds : bond 0.06019 / 3.93 ( 793) hydrogen bonds : angle 6.95876 / 4.73 ( 2244) Misc. bond : bond 0.00335 / 0.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 930 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.9346 (p) cc_final: 0.9126 (m) REVERT: A 43 THR cc_start: 0.8979 (p) cc_final: 0.8531 (t) REVERT: A 110 THR cc_start: 0.7651 (p) cc_final: 0.7287 (t) REVERT: A 131 ASN cc_start: 0.7158 (m-40) cc_final: 0.6897 (m-40) REVERT: A 133 ASN cc_start: 0.8321 (m-40) cc_final: 0.7700 (m-40) REVERT: A 155 LYS cc_start: 0.8538 (ptpt) cc_final: 0.7837 (tptt) REVERT: A 200 THR cc_start: 0.8512 (m) cc_final: 0.8189 (p) REVERT: A 208 VAL cc_start: 0.8584 (t) cc_final: 0.8379 (t) REVERT: B 43 THR cc_start: 0.8075 (p) cc_final: 0.7579 (m) REVERT: B 49 GLN cc_start: 0.7742 (mt0) cc_final: 0.7252 (mm-40) REVERT: B 97 SER cc_start: 0.8064 (p) cc_final: 0.7762 (p) REVERT: B 182 ILE cc_start: 0.9422 (tp) cc_final: 0.8988 (tt) REVERT: C 48 THR cc_start: 0.7820 (p) cc_final: 0.7297 (p) REVERT: C 178 PRO cc_start: 0.8981 (Cg_exo) cc_final: 0.8702 (Cg_endo) REVERT: D 92 THR cc_start: 0.9560 (m) cc_final: 0.9041 (t) REVERT: D 108 GLU cc_start: 0.7539 (tp30) cc_final: 0.6931 (tp30) REVERT: D 132 THR cc_start: 0.8861 (m) cc_final: 0.8586 (m) REVERT: D 133 ASN cc_start: 0.8302 (m-40) cc_final: 0.7305 (m-40) REVERT: D 172 PHE cc_start: 0.8360 (m-80) cc_final: 0.8150 (m-80) REVERT: D 200 THR cc_start: 0.8743 (m) cc_final: 0.8311 (p) REVERT: E 105 LEU cc_start: 0.7870 (mm) cc_final: 0.7415 (mm) REVERT: E 110 THR cc_start: 0.8088 (p) cc_final: 0.7484 (t) REVERT: E 143 ASP cc_start: 0.7704 (t0) cc_final: 0.7497 (t0) REVERT: E 176 ILE cc_start: 0.8174 (pt) cc_final: 0.7946 (mt) REVERT: E 186 VAL cc_start: 0.9225 (t) cc_final: 0.8947 (m) REVERT: E 200 THR cc_start: 0.8742 (m) cc_final: 0.8328 (p) REVERT: F 112 TYR cc_start: 0.7326 (m-80) cc_final: 0.6764 (m-10) REVERT: G 36 LEU cc_start: 0.7982 (mt) cc_final: 0.7740 (mt) REVERT: G 203 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8104 (m) REVERT: H 139 LEU cc_start: 0.8518 (pp) cc_final: 0.8218 (pp) REVERT: H 181 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8352 (tptt) REVERT: H 185 LYS cc_start: 0.8926 (ptmt) cc_final: 0.8684 (pttm) REVERT: H 200 THR cc_start: 0.8316 (m) cc_final: 0.7890 (p) REVERT: I 66 SER cc_start: 0.7682 (m) cc_final: 0.7223 (p) REVERT: I 110 THR cc_start: 0.7716 (p) cc_final: 0.7129 (t) REVERT: I 112 TYR cc_start: 0.7983 (m-80) cc_final: 0.7399 (m-80) REVERT: I 158 ILE cc_start: 0.9501 (mt) cc_final: 0.8985 (tp) REVERT: I 200 THR cc_start: 0.8485 (m) cc_final: 0.8221 (p) REVERT: J 18 MET cc_start: 0.6179 (ttt) cc_final: 0.4866 (ptp) REVERT: J 93 ARG cc_start: 0.8600 (mpt90) cc_final: 0.7247 (mmt180) REVERT: J 127 TRP cc_start: 0.7159 (m100) cc_final: 0.6674 (m100) REVERT: K 36 LEU cc_start: 0.7996 (mt) cc_final: 0.7792 (mt) REVERT: K 210 GLU cc_start: 0.8632 (pm20) cc_final: 0.8082 (pm20) REVERT: L 56 LYS cc_start: 0.8739 (pttp) cc_final: 0.8425 (ptpp) REVERT: M 113 HIS cc_start: 0.7391 (t70) cc_final: 0.7170 (t70) REVERT: M 133 ASN cc_start: 0.8098 (m-40) cc_final: 0.7796 (m-40) REVERT: M 172 PHE cc_start: 0.8190 (m-80) cc_final: 0.6225 (t80) REVERT: M 200 THR cc_start: 0.8586 (m) cc_final: 0.8352 (p) REVERT: N 106 LYS cc_start: 0.8255 (ttpp) cc_final: 0.7871 (tttt) REVERT: N 112 TYR cc_start: 0.7978 (m-80) cc_final: 0.7521 (m-10) REVERT: O 98 ASN cc_start: 0.8133 (t0) cc_final: 0.7328 (t0) REVERT: P 18 MET cc_start: 0.6749 (ttt) cc_final: 0.6207 (ttm) REVERT: P 66 SER cc_start: 0.6406 (m) cc_final: 0.5871 (t) REVERT: P 89 LEU cc_start: 0.8053 (mt) cc_final: 0.7806 (mt) REVERT: P 132 THR cc_start: 0.8320 (m) cc_final: 0.8066 (m) REVERT: P 140 GLN cc_start: 0.6360 (tt0) cc_final: 0.5412 (mm110) outliers start: 10 outliers final: 5 residues processed: 936 average time/residue: 0.1358 time to fit residues: 210.3416 Evaluate side-chains 821 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 815 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 185 optimal weight: 6.9990 chunk 281 optimal weight: 0.9980 chunk 294 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 113 HIS ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 91 ASN D 113 HIS E 41 GLN E 133 ASN ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 HIS J 113 HIS J 133 ASN K 91 ASN K 149 ASN M 91 ASN M 149 ASN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN P 41 GLN P 49 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.175461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.163184 restraints weight = 33057.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.166175 restraints weight = 20343.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.168117 restraints weight = 13516.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.169414 restraints weight = 9572.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.170438 restraints weight = 7146.066| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24884 Z= 0.192 Angle : 0.769 9.998 33904 Z= 0.409 Chirality : 0.055 0.397 4208 Planarity : 0.006 0.061 4320 Dihedral : 7.320 29.498 3456 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer: Outliers : 0.33 % Allowed : 7.70 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.13), residues: 3280 helix: -0.33 (0.19), residues: 704 sheet: -3.02 (0.18), residues: 576 loop : -3.41 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 179 TYR 0.028 0.002 TYR D 112 PHE 0.027 0.003 PHE C 198 TRP 0.028 0.004 TRP G 127 HIS 0.013 0.003 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (24880) covalent geometry : angle 0.76874 / 0.41 (33904) hydrogen bonds : bond 0.05013 / 3.27 ( 793) hydrogen bonds : angle 6.41646 / 4.37 ( 2244) Misc. bond : bond 0.00720 / 0.34 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 907 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.9050 (p) cc_final: 0.8595 (t) REVERT: A 49 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.6016 (mm-40) REVERT: A 110 THR cc_start: 0.7527 (p) cc_final: 0.7195 (t) REVERT: A 131 ASN cc_start: 0.6906 (m-40) cc_final: 0.6665 (m110) REVERT: A 133 ASN cc_start: 0.8394 (m-40) cc_final: 0.7791 (m-40) REVERT: A 155 LYS cc_start: 0.8440 (ptpt) cc_final: 0.7876 (tptt) REVERT: A 171 VAL cc_start: 0.8696 (p) cc_final: 0.8130 (t) REVERT: A 174 LYS cc_start: 0.7082 (mptt) cc_final: 0.6803 (mmtp) REVERT: A 200 THR cc_start: 0.8572 (m) cc_final: 0.8291 (p) REVERT: B 43 THR cc_start: 0.8068 (p) cc_final: 0.7843 (m) REVERT: B 49 GLN cc_start: 0.7903 (mt0) cc_final: 0.7438 (mm-40) REVERT: C 178 PRO cc_start: 0.8951 (Cg_exo) cc_final: 0.8728 (Cg_endo) REVERT: D 92 THR cc_start: 0.9542 (m) cc_final: 0.9056 (t) REVERT: D 108 GLU cc_start: 0.7407 (tp30) cc_final: 0.6865 (tp30) REVERT: D 132 THR cc_start: 0.8873 (m) cc_final: 0.8467 (m) REVERT: D 133 ASN cc_start: 0.8211 (m-40) cc_final: 0.7091 (m-40) REVERT: D 172 PHE cc_start: 0.8396 (m-80) cc_final: 0.8145 (m-80) REVERT: D 200 THR cc_start: 0.8803 (m) cc_final: 0.8193 (p) REVERT: E 105 LEU cc_start: 0.7932 (mm) cc_final: 0.7617 (mm) REVERT: E 110 THR cc_start: 0.8096 (p) cc_final: 0.7517 (t) REVERT: E 179 ARG cc_start: 0.7721 (ptp-110) cc_final: 0.7487 (ptp90) REVERT: E 200 THR cc_start: 0.8685 (m) cc_final: 0.8383 (p) REVERT: F 112 TYR cc_start: 0.7418 (m-80) cc_final: 0.6603 (m-10) REVERT: G 18 MET cc_start: 0.6807 (tpp) cc_final: 0.6492 (tpt) REVERT: G 36 LEU cc_start: 0.7914 (mt) cc_final: 0.7701 (mt) REVERT: H 55 ILE cc_start: 0.9120 (mt) cc_final: 0.8853 (mm) REVERT: H 181 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8282 (tptt) REVERT: H 200 THR cc_start: 0.8304 (m) cc_final: 0.7886 (p) REVERT: I 37 GLN cc_start: 0.7308 (tm-30) cc_final: 0.7039 (tm-30) REVERT: I 66 SER cc_start: 0.7495 (m) cc_final: 0.7141 (p) REVERT: I 110 THR cc_start: 0.7639 (p) cc_final: 0.7084 (t) REVERT: I 112 TYR cc_start: 0.8182 (m-80) cc_final: 0.7699 (m-80) REVERT: I 113 HIS cc_start: 0.7975 (t70) cc_final: 0.7742 (t-90) REVERT: I 158 ILE cc_start: 0.9526 (mt) cc_final: 0.9023 (tp) REVERT: I 182 ILE cc_start: 0.9184 (tp) cc_final: 0.8857 (tt) REVERT: I 200 THR cc_start: 0.8419 (m) cc_final: 0.8167 (p) REVERT: J 18 MET cc_start: 0.5687 (ttt) cc_final: 0.4616 (ptp) REVERT: J 91 ASN cc_start: 0.7883 (m110) cc_final: 0.7388 (m-40) REVERT: J 127 TRP cc_start: 0.7277 (m100) cc_final: 0.7053 (m100) REVERT: K 112 TYR cc_start: 0.7672 (m-80) cc_final: 0.7470 (m-10) REVERT: L 98 ASN cc_start: 0.5298 (t0) cc_final: 0.4827 (t0) REVERT: L 183 THR cc_start: 0.8593 (m) cc_final: 0.8129 (p) REVERT: M 106 LYS cc_start: 0.8283 (ttpp) cc_final: 0.8083 (tttt) REVERT: M 133 ASN cc_start: 0.8101 (m-40) cc_final: 0.7802 (m-40) REVERT: M 179 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7287 (ptp90) REVERT: M 182 ILE cc_start: 0.8964 (tp) cc_final: 0.8653 (tt) REVERT: N 48 THR cc_start: 0.7869 (p) cc_final: 0.7410 (t) REVERT: N 106 LYS cc_start: 0.7999 (ttpp) cc_final: 0.7798 (tttt) REVERT: N 172 PHE cc_start: 0.7470 (m-80) cc_final: 0.5393 (t80) REVERT: O 98 ASN cc_start: 0.8142 (t0) cc_final: 0.7241 (t0) REVERT: O 197 GLU cc_start: 0.7789 (tt0) cc_final: 0.7494 (tt0) REVERT: P 18 MET cc_start: 0.6461 (ttt) cc_final: 0.5850 (ttm) REVERT: P 66 SER cc_start: 0.6316 (m) cc_final: 0.5804 (t) REVERT: P 79 SER cc_start: 0.9256 (t) cc_final: 0.8787 (p) REVERT: P 140 GLN cc_start: 0.6407 (tt0) cc_final: 0.5444 (mm110) REVERT: P 174 LYS cc_start: 0.6744 (mttp) cc_final: 0.5838 (mmtm) outliers start: 9 outliers final: 3 residues processed: 915 average time/residue: 0.1390 time to fit residues: 210.7975 Evaluate side-chains 796 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 792 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 14 optimal weight: 0.0980 chunk 271 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 256 optimal weight: 5.9990 chunk 213 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 140 GLN B 49 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 91 ASN D 148 GLN E 41 GLN E 140 GLN H 91 ASN ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN J 113 HIS J 133 ASN K 91 ASN L 91 ASN M 102 GLN ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 149 ASN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 149 ASN O 41 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 GLN P 113 HIS P 133 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.174161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.161615 restraints weight = 32960.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.164647 restraints weight = 20399.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.166662 restraints weight = 13606.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.168044 restraints weight = 9602.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.168894 restraints weight = 7232.568| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24884 Z= 0.199 Angle : 0.772 9.339 33904 Z= 0.409 Chirality : 0.056 0.405 4208 Planarity : 0.006 0.066 4320 Dihedral : 7.196 30.131 3456 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.92 % Favored : 83.08 % Rotamer: Outliers : 0.22 % Allowed : 5.65 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.13), residues: 3280 helix: 0.08 (0.19), residues: 704 sheet: -2.91 (0.18), residues: 576 loop : -3.43 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 93 TYR 0.022 0.002 TYR A 204 PHE 0.026 0.003 PHE C 198 TRP 0.029 0.004 TRP K 127 HIS 0.018 0.004 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (24880) covalent geometry : angle 0.77181 / 0.41 (33904) hydrogen bonds : bond 0.04674 / 3.06 ( 793) hydrogen bonds : angle 6.19493 / 4.22 ( 2244) Misc. bond : bond 0.00350 / 0.17 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 891 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.9104 (p) cc_final: 0.8674 (t) REVERT: A 110 THR cc_start: 0.7557 (p) cc_final: 0.7257 (t) REVERT: A 131 ASN cc_start: 0.6905 (m-40) cc_final: 0.6449 (m-40) REVERT: A 133 ASN cc_start: 0.8431 (m-40) cc_final: 0.7835 (m-40) REVERT: A 155 LYS cc_start: 0.8398 (ptpt) cc_final: 0.7930 (tptt) REVERT: A 171 VAL cc_start: 0.8886 (p) cc_final: 0.8352 (t) REVERT: A 174 LYS cc_start: 0.7126 (mptt) cc_final: 0.6832 (mmtp) REVERT: A 200 THR cc_start: 0.8642 (m) cc_final: 0.8317 (p) REVERT: B 43 THR cc_start: 0.7931 (p) cc_final: 0.7651 (m) REVERT: B 49 GLN cc_start: 0.7769 (mt0) cc_final: 0.7292 (mm-40) REVERT: B 158 ILE cc_start: 0.9236 (mt) cc_final: 0.9032 (mt) REVERT: C 155 LYS cc_start: 0.8496 (ptpp) cc_final: 0.8134 (ptpp) REVERT: D 92 THR cc_start: 0.9503 (m) cc_final: 0.9087 (t) REVERT: D 132 THR cc_start: 0.8905 (m) cc_final: 0.8613 (m) REVERT: D 172 PHE cc_start: 0.8550 (m-80) cc_final: 0.8253 (m-80) REVERT: D 200 THR cc_start: 0.8794 (m) cc_final: 0.8358 (p) REVERT: E 105 LEU cc_start: 0.7827 (mm) cc_final: 0.7517 (mm) REVERT: E 110 THR cc_start: 0.8143 (p) cc_final: 0.7526 (t) REVERT: E 143 ASP cc_start: 0.7677 (t0) cc_final: 0.7471 (t0) REVERT: E 185 LYS cc_start: 0.8645 (ptmt) cc_final: 0.8206 (pttm) REVERT: E 200 THR cc_start: 0.8683 (m) cc_final: 0.8429 (p) REVERT: F 73 LYS cc_start: 0.7709 (tttt) cc_final: 0.7500 (tttt) REVERT: F 132 THR cc_start: 0.8671 (p) cc_final: 0.8456 (p) REVERT: G 36 LEU cc_start: 0.7951 (mt) cc_final: 0.7662 (mt) REVERT: G 81 ASN cc_start: 0.8832 (m-40) cc_final: 0.8620 (m110) REVERT: G 84 SER cc_start: 0.8278 (m) cc_final: 0.8050 (m) REVERT: G 95 VAL cc_start: 0.9142 (t) cc_final: 0.8905 (m) REVERT: G 107 TYR cc_start: 0.8366 (t80) cc_final: 0.7842 (t80) REVERT: G 136 ILE cc_start: 0.9041 (tp) cc_final: 0.8804 (tp) REVERT: G 200 THR cc_start: 0.8707 (m) cc_final: 0.8398 (p) REVERT: H 18 MET cc_start: 0.6143 (mmm) cc_final: 0.5811 (mmm) REVERT: H 167 GLU cc_start: 0.6165 (pp20) cc_final: 0.5772 (pp20) REVERT: H 174 LYS cc_start: 0.7470 (mttp) cc_final: 0.7258 (pttp) REVERT: H 200 THR cc_start: 0.8385 (m) cc_final: 0.8011 (p) REVERT: I 37 GLN cc_start: 0.7450 (tm-30) cc_final: 0.6919 (tm-30) REVERT: I 66 SER cc_start: 0.7707 (m) cc_final: 0.7427 (p) REVERT: I 110 THR cc_start: 0.7713 (p) cc_final: 0.7117 (t) REVERT: I 112 TYR cc_start: 0.8342 (m-80) cc_final: 0.7975 (m-80) REVERT: I 158 ILE cc_start: 0.9512 (mt) cc_final: 0.9037 (mm) REVERT: I 182 ILE cc_start: 0.9155 (tp) cc_final: 0.8847 (tt) REVERT: I 200 THR cc_start: 0.8535 (m) cc_final: 0.8121 (p) REVERT: J 13 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8367 (mp) REVERT: J 18 MET cc_start: 0.5580 (ttt) cc_final: 0.4547 (ptp) REVERT: J 108 GLU cc_start: 0.6509 (tm-30) cc_final: 0.6303 (tm-30) REVERT: K 112 TYR cc_start: 0.7912 (m-80) cc_final: 0.7500 (m-10) REVERT: L 183 THR cc_start: 0.8457 (m) cc_final: 0.8036 (p) REVERT: M 73 LYS cc_start: 0.8276 (mttt) cc_final: 0.7955 (mtmm) REVERT: M 106 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8053 (tttt) REVERT: M 133 ASN cc_start: 0.8102 (m-40) cc_final: 0.7800 (m-40) REVERT: M 179 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7309 (ptp90) REVERT: N 18 MET cc_start: 0.8100 (mtm) cc_final: 0.7815 (mtm) REVERT: N 48 THR cc_start: 0.8030 (p) cc_final: 0.7555 (t) REVERT: N 72 GLU cc_start: 0.7950 (pm20) cc_final: 0.7394 (pm20) REVERT: N 106 LYS cc_start: 0.7937 (ttpp) cc_final: 0.7678 (tttt) REVERT: N 172 PHE cc_start: 0.7568 (m-80) cc_final: 0.5643 (t80) REVERT: O 98 ASN cc_start: 0.8129 (t0) cc_final: 0.7703 (t0) REVERT: O 202 SER cc_start: 0.7549 (m) cc_final: 0.7143 (m) REVERT: P 18 MET cc_start: 0.6387 (ttt) cc_final: 0.5965 (mtm) REVERT: P 69 THR cc_start: 0.7601 (m) cc_final: 0.7245 (m) REVERT: P 79 SER cc_start: 0.9319 (t) cc_final: 0.8702 (p) REVERT: P 132 THR cc_start: 0.8223 (m) cc_final: 0.7975 (m) REVERT: P 140 GLN cc_start: 0.6637 (tt0) cc_final: 0.5397 (mm110) REVERT: P 172 PHE cc_start: 0.7476 (m-10) cc_final: 0.6214 (m-80) REVERT: P 182 ILE cc_start: 0.8726 (tp) cc_final: 0.8482 (tp) outliers start: 6 outliers final: 1 residues processed: 894 average time/residue: 0.1385 time to fit residues: 204.9490 Evaluate side-chains 799 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 797 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 167 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN C 133 ASN E 41 GLN E 133 ASN F 81 ASN H 31 GLN H 140 GLN I 140 GLN J 133 ASN K 31 GLN M 91 ASN M 133 ASN M 149 ASN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN P 49 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.180483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.168180 restraints weight = 32485.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.171228 restraints weight = 20215.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.173217 restraints weight = 13497.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.174600 restraints weight = 9542.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.175415 restraints weight = 7082.501| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24884 Z= 0.150 Angle : 0.725 9.542 33904 Z= 0.381 Chirality : 0.054 0.433 4208 Planarity : 0.005 0.061 4320 Dihedral : 6.788 28.374 3456 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.13), residues: 3280 helix: 0.21 (0.19), residues: 736 sheet: -2.79 (0.18), residues: 576 loop : -3.35 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 179 TYR 0.019 0.001 TYR A 112 PHE 0.044 0.003 PHE C 198 TRP 0.031 0.004 TRP J 127 HIS 0.015 0.003 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (24880) covalent geometry : angle 0.72508 / 0.38 (33904) hydrogen bonds : bond 0.04239 / 2.77 ( 793) hydrogen bonds : angle 5.95939 / 4.06 ( 2244) Misc. bond : bond 0.00629 / 0.28 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 866 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.9082 (p) cc_final: 0.8652 (t) REVERT: A 131 ASN cc_start: 0.6544 (m-40) cc_final: 0.6123 (m-40) REVERT: A 133 ASN cc_start: 0.8323 (m-40) cc_final: 0.7721 (m-40) REVERT: A 155 LYS cc_start: 0.8461 (ptpt) cc_final: 0.7900 (tptt) REVERT: A 174 LYS cc_start: 0.7015 (mptt) cc_final: 0.6654 (mmtp) REVERT: A 200 THR cc_start: 0.8449 (m) cc_final: 0.8134 (p) REVERT: B 49 GLN cc_start: 0.7217 (mt0) cc_final: 0.6813 (mm-40) REVERT: C 155 LYS cc_start: 0.8455 (ptpp) cc_final: 0.8132 (ptpp) REVERT: D 92 THR cc_start: 0.9449 (m) cc_final: 0.9049 (t) REVERT: D 108 GLU cc_start: 0.7398 (tp30) cc_final: 0.7142 (tp30) REVERT: D 132 THR cc_start: 0.8720 (m) cc_final: 0.8418 (m) REVERT: D 133 ASN cc_start: 0.8177 (m-40) cc_final: 0.7316 (m-40) REVERT: D 200 THR cc_start: 0.8726 (m) cc_final: 0.8247 (p) REVERT: E 185 LYS cc_start: 0.8693 (ptmt) cc_final: 0.8195 (pttm) REVERT: E 200 THR cc_start: 0.8677 (m) cc_final: 0.8287 (p) REVERT: F 189 GLU cc_start: 0.7830 (tt0) cc_final: 0.7567 (tt0) REVERT: G 144 ASN cc_start: 0.8233 (m-40) cc_final: 0.7944 (m110) REVERT: G 181 LYS cc_start: 0.8517 (tppp) cc_final: 0.7659 (tppt) REVERT: G 200 THR cc_start: 0.8670 (m) cc_final: 0.8269 (p) REVERT: H 200 THR cc_start: 0.8151 (m) cc_final: 0.7739 (p) REVERT: I 18 MET cc_start: 0.6766 (ttt) cc_final: 0.6558 (ttp) REVERT: I 64 THR cc_start: 0.8027 (t) cc_final: 0.7786 (t) REVERT: I 66 SER cc_start: 0.7644 (m) cc_final: 0.7326 (p) REVERT: I 110 THR cc_start: 0.8015 (p) cc_final: 0.7395 (t) REVERT: I 112 TYR cc_start: 0.8217 (m-80) cc_final: 0.7967 (m-80) REVERT: I 158 ILE cc_start: 0.9496 (mt) cc_final: 0.9052 (mm) REVERT: I 200 THR cc_start: 0.8412 (m) cc_final: 0.8088 (p) REVERT: I 204 TYR cc_start: 0.7045 (p90) cc_final: 0.6458 (p90) REVERT: J 18 MET cc_start: 0.5411 (ttt) cc_final: 0.4675 (mtm) REVERT: J 172 PHE cc_start: 0.6844 (m-80) cc_final: 0.4426 (t80) REVERT: K 112 TYR cc_start: 0.7694 (m-80) cc_final: 0.7354 (m-10) REVERT: L 98 ASN cc_start: 0.5153 (t0) cc_final: 0.4734 (t0) REVERT: L 109 LYS cc_start: 0.8394 (mppt) cc_final: 0.8126 (mppt) REVERT: L 183 THR cc_start: 0.8491 (m) cc_final: 0.8195 (p) REVERT: M 106 LYS cc_start: 0.8272 (ttpp) cc_final: 0.8060 (tttt) REVERT: M 110 THR cc_start: 0.7732 (p) cc_final: 0.7104 (t) REVERT: M 127 TRP cc_start: 0.7872 (m100) cc_final: 0.7606 (m100) REVERT: M 133 ASN cc_start: 0.8003 (m110) cc_final: 0.7771 (m-40) REVERT: N 18 MET cc_start: 0.7877 (mtm) cc_final: 0.7476 (mtm) REVERT: N 48 THR cc_start: 0.7970 (p) cc_final: 0.7414 (t) REVERT: N 72 GLU cc_start: 0.7766 (pm20) cc_final: 0.7219 (pm20) REVERT: N 132 THR cc_start: 0.8286 (m) cc_final: 0.8030 (m) REVERT: N 172 PHE cc_start: 0.7512 (m-80) cc_final: 0.5644 (t80) REVERT: O 98 ASN cc_start: 0.8095 (t0) cc_final: 0.7749 (t0) REVERT: O 112 TYR cc_start: 0.7905 (m-10) cc_final: 0.7661 (m-10) REVERT: P 18 MET cc_start: 0.6052 (ttt) cc_final: 0.5424 (mtm) REVERT: P 69 THR cc_start: 0.7667 (m) cc_final: 0.7425 (m) REVERT: P 79 SER cc_start: 0.9257 (t) cc_final: 0.8759 (p) REVERT: P 140 GLN cc_start: 0.6551 (tt0) cc_final: 0.5504 (mm110) outliers start: 2 outliers final: 0 residues processed: 867 average time/residue: 0.1334 time to fit residues: 193.9074 Evaluate side-chains 773 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 773 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 282 optimal weight: 0.0030 chunk 146 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN B 49 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 133 ASN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 140 GLN J 113 HIS L 31 GLN L 91 ASN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN O 41 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 ASN ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.180707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.168438 restraints weight = 32598.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.171451 restraints weight = 20211.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.173470 restraints weight = 13487.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.174853 restraints weight = 9522.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.175714 restraints weight = 7058.695| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24884 Z= 0.158 Angle : 0.732 9.802 33904 Z= 0.384 Chirality : 0.055 0.435 4208 Planarity : 0.005 0.065 4320 Dihedral : 6.693 28.178 3456 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.82 % Favored : 84.18 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.13), residues: 3280 helix: 0.40 (0.19), residues: 736 sheet: -2.69 (0.18), residues: 576 loop : -3.33 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 179 TYR 0.040 0.002 TYR P 70 PHE 0.034 0.003 PHE D 121 TRP 0.030 0.003 TRP J 127 HIS 0.013 0.003 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (24880) covalent geometry : angle 0.73194 / 0.38 (33904) hydrogen bonds : bond 0.04124 / 2.70 ( 793) hydrogen bonds : angle 5.84537 / 3.97 ( 2244) Misc. bond : bond 0.00375 / 0.18 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 870 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASN cc_start: 0.6304 (m-40) cc_final: 0.5761 (m-40) REVERT: A 133 ASN cc_start: 0.8330 (m-40) cc_final: 0.7762 (m-40) REVERT: A 155 LYS cc_start: 0.8516 (ptpt) cc_final: 0.7920 (tptt) REVERT: A 174 LYS cc_start: 0.7065 (mptt) cc_final: 0.6688 (mmtp) REVERT: A 200 THR cc_start: 0.8499 (m) cc_final: 0.8157 (p) REVERT: B 49 GLN cc_start: 0.7332 (mt0) cc_final: 0.7041 (mm-40) REVERT: C 33 SER cc_start: 0.8480 (m) cc_final: 0.8103 (p) REVERT: C 155 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8150 (ptpp) REVERT: D 92 THR cc_start: 0.9463 (m) cc_final: 0.8826 (t) REVERT: D 108 GLU cc_start: 0.7414 (tp30) cc_final: 0.7140 (tp30) REVERT: D 132 THR cc_start: 0.8749 (m) cc_final: 0.8436 (m) REVERT: D 133 ASN cc_start: 0.8117 (m-40) cc_final: 0.7299 (m-40) REVERT: D 200 THR cc_start: 0.8694 (m) cc_final: 0.8213 (p) REVERT: E 143 ASP cc_start: 0.7648 (t0) cc_final: 0.7428 (t0) REVERT: E 179 ARG cc_start: 0.7922 (mtm-85) cc_final: 0.7355 (ttm-80) REVERT: E 185 LYS cc_start: 0.8668 (ptmt) cc_final: 0.8208 (pttm) REVERT: F 132 THR cc_start: 0.8395 (p) cc_final: 0.8163 (p) REVERT: F 189 GLU cc_start: 0.7801 (tt0) cc_final: 0.7467 (tt0) REVERT: G 144 ASN cc_start: 0.8249 (m-40) cc_final: 0.7984 (m110) REVERT: G 181 LYS cc_start: 0.8487 (tppp) cc_final: 0.7666 (tppt) REVERT: G 200 THR cc_start: 0.8791 (m) cc_final: 0.8396 (p) REVERT: H 200 THR cc_start: 0.8248 (m) cc_final: 0.7773 (p) REVERT: I 64 THR cc_start: 0.8057 (t) cc_final: 0.7817 (t) REVERT: I 66 SER cc_start: 0.7641 (m) cc_final: 0.7370 (p) REVERT: I 110 THR cc_start: 0.8052 (p) cc_final: 0.7490 (t) REVERT: I 112 TYR cc_start: 0.8307 (m-80) cc_final: 0.7922 (m-80) REVERT: I 158 ILE cc_start: 0.9491 (mt) cc_final: 0.9010 (mm) REVERT: I 182 ILE cc_start: 0.9051 (tp) cc_final: 0.8599 (tt) REVERT: I 200 THR cc_start: 0.8411 (m) cc_final: 0.8056 (p) REVERT: I 204 TYR cc_start: 0.7105 (p90) cc_final: 0.6518 (p90) REVERT: J 18 MET cc_start: 0.5490 (ttt) cc_final: 0.4738 (mtm) REVERT: J 172 PHE cc_start: 0.7008 (m-80) cc_final: 0.4538 (t80) REVERT: K 43 THR cc_start: 0.8174 (p) cc_final: 0.7973 (p) REVERT: K 112 TYR cc_start: 0.7836 (m-80) cc_final: 0.7331 (m-10) REVERT: L 179 ARG cc_start: 0.7651 (mtt-85) cc_final: 0.7292 (mtt-85) REVERT: L 183 THR cc_start: 0.8553 (m) cc_final: 0.8144 (p) REVERT: M 110 THR cc_start: 0.7627 (p) cc_final: 0.7188 (t) REVERT: M 127 TRP cc_start: 0.7823 (m100) cc_final: 0.7550 (m100) REVERT: M 133 ASN cc_start: 0.8101 (m110) cc_final: 0.7810 (m-40) REVERT: M 179 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7180 (ptp90) REVERT: N 48 THR cc_start: 0.7903 (p) cc_final: 0.7390 (t) REVERT: N 72 GLU cc_start: 0.7789 (pm20) cc_final: 0.7392 (pm20) REVERT: N 172 PHE cc_start: 0.7574 (m-80) cc_final: 0.5875 (t80) REVERT: O 98 ASN cc_start: 0.7982 (t0) cc_final: 0.7673 (t0) REVERT: P 18 MET cc_start: 0.5981 (ttt) cc_final: 0.5153 (mtp) REVERT: P 132 THR cc_start: 0.8257 (m) cc_final: 0.7863 (m) REVERT: P 140 GLN cc_start: 0.6490 (tt0) cc_final: 0.5416 (mm110) outliers start: 0 outliers final: 0 residues processed: 870 average time/residue: 0.1361 time to fit residues: 196.9416 Evaluate side-chains 757 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 757 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 175 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 258 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 303 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN B 81 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN J 133 ASN L 31 GLN M 91 ASN M 113 HIS ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN O 41 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.179197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.167148 restraints weight = 32443.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.170077 restraints weight = 20458.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.172004 restraints weight = 13824.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.173312 restraints weight = 9880.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.174158 restraints weight = 7420.708| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24884 Z= 0.195 Angle : 0.771 9.932 33904 Z= 0.407 Chirality : 0.056 0.485 4208 Planarity : 0.006 0.072 4320 Dihedral : 6.790 29.891 3456 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.68 % Favored : 83.32 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.13), residues: 3280 helix: 0.44 (0.19), residues: 736 sheet: -2.39 (0.18), residues: 672 loop : -3.45 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 179 TYR 0.024 0.002 TYR L 35 PHE 0.026 0.003 PHE F 198 TRP 0.034 0.005 TRP D 127 HIS 0.016 0.003 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (24880) covalent geometry : angle 0.77092 / 0.41 (33904) hydrogen bonds : bond 0.04203 / 2.75 ( 793) hydrogen bonds : angle 5.91032 / 4.01 ( 2244) Misc. bond : bond 0.00304 / 0.15 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 866 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.9121 (p) cc_final: 0.8646 (t) REVERT: A 155 LYS cc_start: 0.8618 (ptpt) cc_final: 0.7998 (tptt) REVERT: A 174 LYS cc_start: 0.7127 (mptt) cc_final: 0.6769 (mmtp) REVERT: A 200 THR cc_start: 0.8656 (m) cc_final: 0.8261 (p) REVERT: B 49 GLN cc_start: 0.7489 (mt0) cc_final: 0.7039 (mm-40) REVERT: B 127 TRP cc_start: 0.8699 (m100) cc_final: 0.8464 (m-10) REVERT: B 158 ILE cc_start: 0.9226 (mt) cc_final: 0.8986 (mt) REVERT: B 200 THR cc_start: 0.8887 (m) cc_final: 0.8377 (p) REVERT: C 33 SER cc_start: 0.8652 (m) cc_final: 0.8320 (p) REVERT: C 155 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8265 (ptpp) REVERT: C 198 PHE cc_start: 0.9165 (p90) cc_final: 0.8699 (p90) REVERT: D 200 THR cc_start: 0.8713 (m) cc_final: 0.8190 (p) REVERT: E 143 ASP cc_start: 0.7663 (t0) cc_final: 0.7427 (t0) REVERT: E 179 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7400 (ttm-80) REVERT: E 185 LYS cc_start: 0.8759 (ptmt) cc_final: 0.8262 (pttm) REVERT: F 189 GLU cc_start: 0.7877 (tt0) cc_final: 0.7521 (tt0) REVERT: G 144 ASN cc_start: 0.8207 (m-40) cc_final: 0.7951 (m110) REVERT: G 181 LYS cc_start: 0.8603 (tppp) cc_final: 0.7758 (tppt) REVERT: G 200 THR cc_start: 0.8817 (m) cc_final: 0.8452 (p) REVERT: H 200 THR cc_start: 0.8298 (m) cc_final: 0.7918 (p) REVERT: I 66 SER cc_start: 0.7645 (m) cc_final: 0.7405 (p) REVERT: I 110 THR cc_start: 0.7859 (p) cc_final: 0.7282 (t) REVERT: I 158 ILE cc_start: 0.9501 (mt) cc_final: 0.9072 (mm) REVERT: I 200 THR cc_start: 0.8437 (m) cc_final: 0.8228 (p) REVERT: J 18 MET cc_start: 0.5578 (ttt) cc_final: 0.4649 (ptp) REVERT: J 89 LEU cc_start: 0.8917 (mm) cc_final: 0.8703 (mm) REVERT: J 93 ARG cc_start: 0.8201 (mmt180) cc_final: 0.7907 (mmt180) REVERT: K 49 GLN cc_start: 0.7401 (mt0) cc_final: 0.6697 (mt0) REVERT: K 112 TYR cc_start: 0.7756 (m-80) cc_final: 0.7243 (m-10) REVERT: M 68 LYS cc_start: 0.8238 (mmtp) cc_final: 0.7882 (mmtp) REVERT: M 73 LYS cc_start: 0.8058 (mttt) cc_final: 0.7835 (mttp) REVERT: M 110 THR cc_start: 0.7684 (p) cc_final: 0.7265 (t) REVERT: M 127 TRP cc_start: 0.7913 (m100) cc_final: 0.7635 (m100) REVERT: M 133 ASN cc_start: 0.8169 (m110) cc_final: 0.7829 (m-40) REVERT: M 179 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7352 (ptp90) REVERT: N 48 THR cc_start: 0.7931 (p) cc_final: 0.7485 (t) REVERT: N 132 THR cc_start: 0.8380 (m) cc_final: 0.8144 (m) REVERT: N 172 PHE cc_start: 0.7616 (m-80) cc_final: 0.5752 (t80) REVERT: O 98 ASN cc_start: 0.8263 (t0) cc_final: 0.8003 (t0) REVERT: P 18 MET cc_start: 0.6053 (ttt) cc_final: 0.5208 (mtp) REVERT: P 66 SER cc_start: 0.6397 (m) cc_final: 0.5919 (t) REVERT: P 132 THR cc_start: 0.8139 (m) cc_final: 0.7797 (m) REVERT: P 140 GLN cc_start: 0.6696 (tt0) cc_final: 0.5552 (mm110) REVERT: P 172 PHE cc_start: 0.7625 (m-80) cc_final: 0.5636 (t80) outliers start: 0 outliers final: 0 residues processed: 866 average time/residue: 0.1341 time to fit residues: 193.9085 Evaluate side-chains 748 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 748 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 205 optimal weight: 0.8980 chunk 295 optimal weight: 0.5980 chunk 256 optimal weight: 10.0000 chunk 39 optimal weight: 0.0070 chunk 61 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 235 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 102 GLN A 131 ASN A 140 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 ASN L 31 GLN ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 ASN M 31 GLN M 98 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 GLN P 81 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.188463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.179245 restraints weight = 32037.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.181415 restraints weight = 21274.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.182868 restraints weight = 14911.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.183853 restraints weight = 10956.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.184446 restraints weight = 8502.409| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24884 Z= 0.141 Angle : 0.730 10.418 33904 Z= 0.380 Chirality : 0.055 0.425 4208 Planarity : 0.006 0.073 4320 Dihedral : 6.467 30.188 3456 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.36 % Favored : 85.64 % Rotamer: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.14), residues: 3280 helix: 0.63 (0.19), residues: 736 sheet: -2.26 (0.18), residues: 672 loop : -3.36 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 179 TYR 0.027 0.001 TYR L 35 PHE 0.032 0.003 PHE G 172 TRP 0.040 0.004 TRP K 127 HIS 0.006 0.002 HIS O 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (24880) covalent geometry : angle 0.73024 / 0.38 (33904) hydrogen bonds : bond 0.03777 / 2.46 ( 793) hydrogen bonds : angle 5.68117 / 3.85 ( 2244) Misc. bond : bond 0.00263 / 0.12 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 852 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.8530 (ptpt) cc_final: 0.7881 (tptt) REVERT: A 174 LYS cc_start: 0.7011 (mptt) cc_final: 0.6603 (mmtp) REVERT: A 200 THR cc_start: 0.8498 (m) cc_final: 0.8137 (p) REVERT: B 18 MET cc_start: 0.6542 (tpp) cc_final: 0.6299 (mmt) REVERT: B 49 GLN cc_start: 0.7328 (mt0) cc_final: 0.6919 (mm-40) REVERT: B 200 THR cc_start: 0.8635 (m) cc_final: 0.8090 (p) REVERT: C 33 SER cc_start: 0.8598 (m) cc_final: 0.8288 (p) REVERT: D 92 THR cc_start: 0.9360 (m) cc_final: 0.9032 (p) REVERT: D 108 GLU cc_start: 0.7407 (tp30) cc_final: 0.7162 (tp30) REVERT: D 133 ASN cc_start: 0.8042 (m-40) cc_final: 0.7380 (m-40) REVERT: D 200 THR cc_start: 0.8553 (m) cc_final: 0.8048 (p) REVERT: E 179 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7193 (ttm-80) REVERT: E 185 LYS cc_start: 0.8646 (ptmt) cc_final: 0.8113 (pttm) REVERT: F 189 GLU cc_start: 0.7752 (tt0) cc_final: 0.7391 (tt0) REVERT: G 14 VAL cc_start: 0.6281 (t) cc_final: 0.5967 (t) REVERT: G 18 MET cc_start: 0.6009 (tpt) cc_final: 0.5759 (tpt) REVERT: G 144 ASN cc_start: 0.8120 (m-40) cc_final: 0.7782 (m110) REVERT: G 200 THR cc_start: 0.8655 (m) cc_final: 0.8230 (p) REVERT: H 200 THR cc_start: 0.8189 (m) cc_final: 0.7745 (p) REVERT: I 64 THR cc_start: 0.7698 (t) cc_final: 0.7466 (t) REVERT: I 66 SER cc_start: 0.7441 (m) cc_final: 0.7202 (p) REVERT: I 110 THR cc_start: 0.7452 (p) cc_final: 0.6966 (t) REVERT: I 158 ILE cc_start: 0.9473 (mt) cc_final: 0.9073 (mm) REVERT: I 200 THR cc_start: 0.8351 (m) cc_final: 0.8115 (p) REVERT: I 204 TYR cc_start: 0.6910 (p90) cc_final: 0.6415 (p90) REVERT: J 18 MET cc_start: 0.5622 (ttt) cc_final: 0.4848 (mtm) REVERT: J 89 LEU cc_start: 0.8808 (mm) cc_final: 0.8605 (mm) REVERT: K 49 GLN cc_start: 0.7133 (mt0) cc_final: 0.6506 (mt0) REVERT: K 112 TYR cc_start: 0.7666 (m-80) cc_final: 0.7214 (m-10) REVERT: L 179 ARG cc_start: 0.7327 (mtt-85) cc_final: 0.7089 (mtt-85) REVERT: L 183 THR cc_start: 0.8660 (m) cc_final: 0.8324 (p) REVERT: M 73 LYS cc_start: 0.7723 (mttt) cc_final: 0.7513 (mttp) REVERT: M 110 THR cc_start: 0.7248 (p) cc_final: 0.6772 (t) REVERT: M 179 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7236 (ptp90) REVERT: N 48 THR cc_start: 0.7835 (p) cc_final: 0.7440 (t) REVERT: N 132 THR cc_start: 0.8135 (m) cc_final: 0.7911 (m) REVERT: O 98 ASN cc_start: 0.8101 (t0) cc_final: 0.7888 (t0) REVERT: P 18 MET cc_start: 0.6087 (ttt) cc_final: 0.5044 (mtp) REVERT: P 66 SER cc_start: 0.6031 (m) cc_final: 0.5634 (t) REVERT: P 172 PHE cc_start: 0.7337 (m-80) cc_final: 0.5477 (t80) REVERT: P 174 LYS cc_start: 0.7352 (ttpp) cc_final: 0.7090 (ttmt) REVERT: P 181 LYS cc_start: 0.7370 (tppt) cc_final: 0.6851 (tptm) outliers start: 2 outliers final: 0 residues processed: 853 average time/residue: 0.1366 time to fit residues: 196.1932 Evaluate side-chains 751 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 751 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 137 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 307 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 313 optimal weight: 0.2980 chunk 59 optimal weight: 7.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN K 41 GLN L 31 GLN M 91 ASN M 113 HIS ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 149 ASN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 HIS O 37 GLN ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.183325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.173964 restraints weight = 32466.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.176094 restraints weight = 21515.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.177533 restraints weight = 15135.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.178511 restraints weight = 11198.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.179076 restraints weight = 8698.797| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24884 Z= 0.168 Angle : 0.750 10.282 33904 Z= 0.393 Chirality : 0.057 0.474 4208 Planarity : 0.006 0.078 4320 Dihedral : 6.459 28.307 3456 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 0.04 % Allowed : 1.04 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.14), residues: 3280 helix: 0.66 (0.19), residues: 736 sheet: -2.17 (0.18), residues: 672 loop : -3.38 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 179 TYR 0.028 0.002 TYR L 35 PHE 0.021 0.003 PHE D 121 TRP 0.047 0.005 TRP K 127 HIS 0.017 0.003 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (24880) covalent geometry : angle 0.75007 / 0.39 (33904) hydrogen bonds : bond 0.03878 / 2.54 ( 793) hydrogen bonds : angle 5.70125 / 3.87 ( 2244) Misc. bond : bond 0.00551 / 0.27 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 832 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.9147 (p) cc_final: 0.8717 (t) REVERT: A 155 LYS cc_start: 0.8627 (ptpt) cc_final: 0.8003 (tptt) REVERT: A 174 LYS cc_start: 0.7176 (mptt) cc_final: 0.6668 (mmtp) REVERT: A 200 THR cc_start: 0.8513 (m) cc_final: 0.8148 (p) REVERT: B 49 GLN cc_start: 0.7507 (mt0) cc_final: 0.7017 (mm-40) REVERT: B 127 TRP cc_start: 0.8382 (m100) cc_final: 0.8130 (m100) REVERT: B 158 ILE cc_start: 0.9231 (mt) cc_final: 0.9015 (mt) REVERT: B 200 THR cc_start: 0.8753 (m) cc_final: 0.8235 (p) REVERT: D 92 THR cc_start: 0.9385 (m) cc_final: 0.8819 (t) REVERT: D 133 ASN cc_start: 0.8143 (m-40) cc_final: 0.7365 (m-40) REVERT: D 200 THR cc_start: 0.8586 (m) cc_final: 0.8099 (p) REVERT: E 110 THR cc_start: 0.7812 (p) cc_final: 0.7273 (t) REVERT: E 179 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7291 (ttm-80) REVERT: E 185 LYS cc_start: 0.8670 (ptmt) cc_final: 0.8170 (pttm) REVERT: E 200 THR cc_start: 0.8216 (m) cc_final: 0.7654 (p) REVERT: F 114 LYS cc_start: 0.7301 (tptp) cc_final: 0.7060 (tptt) REVERT: F 189 GLU cc_start: 0.7696 (tt0) cc_final: 0.7310 (tt0) REVERT: G 200 THR cc_start: 0.8686 (m) cc_final: 0.8218 (p) REVERT: H 55 ILE cc_start: 0.8775 (mp) cc_final: 0.8547 (mm) REVERT: H 110 THR cc_start: 0.7674 (p) cc_final: 0.7278 (t) REVERT: H 200 THR cc_start: 0.8236 (m) cc_final: 0.7827 (p) REVERT: I 66 SER cc_start: 0.7483 (m) cc_final: 0.7261 (p) REVERT: I 110 THR cc_start: 0.7644 (p) cc_final: 0.7199 (t) REVERT: I 112 TYR cc_start: 0.7473 (m-10) cc_final: 0.7257 (m-80) REVERT: I 158 ILE cc_start: 0.9509 (mt) cc_final: 0.9058 (mm) REVERT: I 200 THR cc_start: 0.8267 (m) cc_final: 0.7951 (p) REVERT: I 204 TYR cc_start: 0.7202 (p90) cc_final: 0.6606 (p90) REVERT: J 18 MET cc_start: 0.5602 (ttt) cc_final: 0.4872 (mtm) REVERT: K 112 TYR cc_start: 0.7672 (m-80) cc_final: 0.7152 (m-10) REVERT: L 109 LYS cc_start: 0.8314 (mppt) cc_final: 0.8017 (mppt) REVERT: L 179 ARG cc_start: 0.7353 (mtt-85) cc_final: 0.7088 (mtt-85) REVERT: M 106 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7924 (tttt) REVERT: M 110 THR cc_start: 0.7507 (p) cc_final: 0.7034 (t) REVERT: M 179 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7269 (ptp90) REVERT: N 48 THR cc_start: 0.7816 (p) cc_final: 0.7331 (t) REVERT: N 69 THR cc_start: 0.8250 (m) cc_final: 0.7779 (m) REVERT: P 18 MET cc_start: 0.6004 (ttt) cc_final: 0.5016 (mtp) REVERT: P 66 SER cc_start: 0.6104 (m) cc_final: 0.5724 (t) REVERT: P 172 PHE cc_start: 0.7460 (m-80) cc_final: 0.5673 (t80) outliers start: 1 outliers final: 0 residues processed: 833 average time/residue: 0.1341 time to fit residues: 186.7874 Evaluate side-chains 722 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 722 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 226 optimal weight: 7.9990 chunk 286 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 220 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN L 91 ASN M 31 GLN M 113 HIS ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN P 49 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.184478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.172243 restraints weight = 32364.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.175270 restraints weight = 20163.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.177263 restraints weight = 13492.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.178568 restraints weight = 9557.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.179599 restraints weight = 7130.848| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24884 Z= 0.161 Angle : 0.755 10.045 33904 Z= 0.395 Chirality : 0.057 0.477 4208 Planarity : 0.006 0.080 4320 Dihedral : 6.510 27.322 3456 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 0.04 % Allowed : 0.56 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.14), residues: 3280 helix: 0.67 (0.19), residues: 736 sheet: -2.11 (0.18), residues: 672 loop : -3.38 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 179 TYR 0.030 0.002 TYR L 35 PHE 0.028 0.003 PHE A 172 TRP 0.040 0.004 TRP K 127 HIS 0.005 0.002 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (24880) covalent geometry : angle 0.75489 / 0.40 (33904) hydrogen bonds : bond 0.03868 / 2.52 ( 793) hydrogen bonds : angle 5.70722 / 3.87 ( 2244) Misc. bond : bond 0.00351 / 0.17 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 800 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.9048 (p) cc_final: 0.8680 (t) REVERT: A 155 LYS cc_start: 0.8596 (ptpt) cc_final: 0.7997 (tptt) REVERT: A 174 LYS cc_start: 0.7250 (mptt) cc_final: 0.6845 (mmtp) REVERT: A 200 THR cc_start: 0.8567 (m) cc_final: 0.8178 (p) REVERT: B 18 MET cc_start: 0.6691 (tpp) cc_final: 0.6280 (mmt) REVERT: B 49 GLN cc_start: 0.7479 (mt0) cc_final: 0.7017 (mm-40) REVERT: B 200 THR cc_start: 0.8716 (m) cc_final: 0.8185 (p) REVERT: D 92 THR cc_start: 0.9340 (m) cc_final: 0.8795 (t) REVERT: D 200 THR cc_start: 0.8624 (m) cc_final: 0.8082 (p) REVERT: E 179 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7323 (ttm-80) REVERT: E 185 LYS cc_start: 0.8678 (ptmt) cc_final: 0.8144 (pttm) REVERT: F 114 LYS cc_start: 0.7284 (tptp) cc_final: 0.7045 (tptt) REVERT: F 189 GLU cc_start: 0.7654 (tt0) cc_final: 0.7267 (tt0) REVERT: G 112 TYR cc_start: 0.7636 (m-80) cc_final: 0.7267 (m-80) REVERT: G 188 PRO cc_start: 0.8388 (Cg_exo) cc_final: 0.8188 (Cg_endo) REVERT: G 200 THR cc_start: 0.8681 (m) cc_final: 0.8209 (p) REVERT: H 110 THR cc_start: 0.7625 (p) cc_final: 0.7189 (t) REVERT: H 200 THR cc_start: 0.8261 (m) cc_final: 0.7827 (p) REVERT: I 64 THR cc_start: 0.7963 (t) cc_final: 0.7725 (t) REVERT: I 66 SER cc_start: 0.7354 (m) cc_final: 0.7093 (p) REVERT: I 110 THR cc_start: 0.7621 (p) cc_final: 0.7139 (t) REVERT: I 112 TYR cc_start: 0.7560 (m-10) cc_final: 0.7137 (m-80) REVERT: I 158 ILE cc_start: 0.9505 (mt) cc_final: 0.9039 (mm) REVERT: I 204 TYR cc_start: 0.7130 (p90) cc_final: 0.6602 (p90) REVERT: J 18 MET cc_start: 0.5644 (ttt) cc_final: 0.4911 (mtp) REVERT: L 179 ARG cc_start: 0.7435 (mtt-85) cc_final: 0.7176 (mtt-85) REVERT: M 106 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7905 (tttt) REVERT: M 110 THR cc_start: 0.7284 (p) cc_final: 0.6877 (t) REVERT: M 179 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7303 (ptp90) REVERT: N 48 THR cc_start: 0.7821 (p) cc_final: 0.7333 (t) REVERT: N 69 THR cc_start: 0.8150 (m) cc_final: 0.7463 (m) REVERT: P 18 MET cc_start: 0.6073 (ttt) cc_final: 0.5047 (mtp) REVERT: P 66 SER cc_start: 0.6250 (m) cc_final: 0.5932 (t) REVERT: P 172 PHE cc_start: 0.7422 (m-80) cc_final: 0.5626 (t80) REVERT: P 174 LYS cc_start: 0.7393 (ttpp) cc_final: 0.6823 (ttmt) REVERT: P 181 LYS cc_start: 0.7609 (tppt) cc_final: 0.7063 (tptm) outliers start: 1 outliers final: 0 residues processed: 801 average time/residue: 0.1324 time to fit residues: 178.4798 Evaluate side-chains 720 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 720 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 225 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 296 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 238 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 98 ASN E 41 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN M 41 GLN M 91 ASN M 113 HIS M 149 ASN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN O 37 GLN P 49 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.186206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.176643 restraints weight = 32422.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.178835 restraints weight = 21537.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.180240 restraints weight = 15226.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.181254 restraints weight = 11305.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.181855 restraints weight = 8917.615| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24884 Z= 0.150 Angle : 0.739 10.735 33904 Z= 0.385 Chirality : 0.055 0.452 4208 Planarity : 0.006 0.080 4320 Dihedral : 6.379 27.036 3456 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 0.04 % Allowed : 0.78 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.14), residues: 3280 helix: 0.74 (0.19), residues: 736 sheet: -1.76 (0.19), residues: 640 loop : -3.44 (0.12), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 179 TYR 0.022 0.001 TYR G 107 PHE 0.024 0.002 PHE J 172 TRP 0.044 0.004 TRP A 127 HIS 0.016 0.002 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (24880) covalent geometry : angle 0.73949 / 0.39 (33904) hydrogen bonds : bond 0.03758 / 2.45 ( 793) hydrogen bonds : angle 5.64418 / 3.83 ( 2244) Misc. bond : bond 0.00300 / 0.14 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4330.06 seconds wall clock time: 75 minutes 49.64 seconds (4549.64 seconds total)