Starting phenix.real_space_refine on Wed Nov 19 12:19:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5o4u_3746/11_2025/5o4u_3746.cif Found real_map, /net/cci-nas-00/data/ceres_data/5o4u_3746/11_2025/5o4u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5o4u_3746/11_2025/5o4u_3746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5o4u_3746/11_2025/5o4u_3746.map" model { file = "/net/cci-nas-00/data/ceres_data/5o4u_3746/11_2025/5o4u_3746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5o4u_3746/11_2025/5o4u_3746.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 6.32, per 1000 atoms: 0.26 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: 2.06 Conformation dependent library (CDL) restraints added in 1.3 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: 0.88 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: 4.52 Time building geometry restraints manager: 2.78 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.230 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 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 covalent geometry : bond 0.00680 (24880) covalent geometry : angle 1.25812 (33904) hydrogen bonds : bond 0.28045 ( 793) hydrogen bonds : angle 10.10555 ( 2244) Misc. bond : bond 0.49480 ( 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 : 0.857 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: 0.7587 (m) REVERT: A 105 LEU cc_start: 0.9265 (mm) cc_final: 0.8871 (mm) REVERT: A 110 THR cc_start: 0.7053 (p) cc_final: 0.6718 (t) REVERT: A 155 LYS cc_start: 0.7322 (ptpt) cc_final: 0.7017 (tptt) REVERT: A 200 THR cc_start: 0.8248 (m) cc_final: 0.7740 (p) REVERT: B 49 GLN cc_start: 0.6468 (mt0) cc_final: 0.6088 (mm-40) REVERT: B 204 TYR cc_start: 0.6842 (p90) cc_final: 0.6589 (p90) REVERT: C 46 GLU cc_start: 0.6349 (mt-10) cc_final: 0.6109 (mt-10) REVERT: C 60 VAL cc_start: 0.9106 (t) cc_final: 0.8849 (m) REVERT: C 150 TYR cc_start: 0.7934 (m-80) cc_final: 0.7565 (m-10) REVERT: D 31 GLN cc_start: 0.6084 (tt0) cc_final: 0.5688 (tt0) REVERT: D 105 LEU cc_start: 0.8285 (mm) cc_final: 0.7992 (mm) REVERT: D 177 PRO cc_start: 0.8999 (Cg_endo) cc_final: 0.8765 (Cg_exo) REVERT: D 200 THR cc_start: 0.8561 (m) cc_final: 0.7882 (p) REVERT: E 105 LEU cc_start: 0.8017 (mm) cc_final: 0.7514 (mm) REVERT: E 110 THR cc_start: 0.8051 (p) cc_final: 0.7429 (t) REVERT: E 150 TYR cc_start: 0.7200 (m-80) cc_final: 0.6906 (m-80) REVERT: E 176 ILE cc_start: 0.8307 (pt) cc_final: 0.7799 (mt) REVERT: E 185 LYS cc_start: 0.8121 (ptmt) cc_final: 0.7839 (pttp) REVERT: E 200 THR cc_start: 0.8555 (m) cc_final: 0.7880 (p) REVERT: F 112 TYR cc_start: 0.7066 (m-80) cc_final: 0.6829 (m-10) REVERT: G 158 ILE cc_start: 0.8934 (mt) cc_final: 0.8655 (mm) REVERT: H 55 ILE cc_start: 0.8683 (mt) cc_final: 0.8406 (mm) REVERT: H 93 ARG cc_start: 0.7584 (mmt-90) cc_final: 0.5989 (mtt180) REVERT: H 139 LEU cc_start: 0.8440 (pp) cc_final: 0.8177 (pp) REVERT: H 158 ILE cc_start: 0.8296 (mt) cc_final: 0.7911 (tt) REVERT: H 185 LYS cc_start: 0.8513 (ptmt) cc_final: 0.8152 (pttm) REVERT: I 64 THR cc_start: 0.6745 (t) cc_final: 0.6511 (t) REVERT: I 66 SER cc_start: 0.7580 (m) cc_final: 0.6805 (p) REVERT: I 110 THR cc_start: 0.6804 (p) cc_final: 0.6528 (t) REVERT: I 158 ILE cc_start: 0.8710 (mt) cc_final: 0.8074 (tp) REVERT: I 200 THR cc_start: 0.8414 (m) cc_final: 0.8189 (t) REVERT: I 204 TYR cc_start: 0.6419 (p90) cc_final: 0.5958 (p90) REVERT: J 16 ILE cc_start: 0.9165 (mt) cc_final: 0.8950 (mt) REVERT: J 18 MET cc_start: 0.5327 (ttt) cc_final: 0.4479 (ptp) REVERT: J 35 TYR cc_start: 0.6011 (t80) cc_final: 0.5577 (t80) REVERT: J 56 LYS cc_start: 0.7885 (pttp) cc_final: 0.7670 (ptpp) REVERT: J 202 SER cc_start: 0.7587 (t) cc_final: 0.7351 (m) REVERT: K 56 LYS cc_start: 0.8535 (pttp) cc_final: 0.8276 (pttm) REVERT: K 210 GLU cc_start: 0.8515 (pm20) cc_final: 0.7988 (pm20) REVERT: L 35 TYR cc_start: 0.6806 (t80) cc_final: 0.6012 (t80) REVERT: L 36 LEU cc_start: 0.7463 (mt) cc_final: 0.6916 (mt) REVERT: L 56 LYS cc_start: 0.8238 (pttp) cc_final: 0.7973 (pttm) REVERT: L 183 THR cc_start: 0.8156 (m) cc_final: 0.7782 (p) REVERT: L 202 SER cc_start: 0.5846 (p) cc_final: 0.5170 (p) REVERT: M 73 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7902 (mtmm) REVERT: M 92 THR cc_start: 0.8435 (m) cc_final: 0.8163 (m) REVERT: M 155 LYS cc_start: 0.6981 (ptpt) cc_final: 0.6725 (ptmt) REVERT: M 179 ARG cc_start: 0.6798 (ttp-110) cc_final: 0.6333 (ptp90) REVERT: M 183 THR cc_start: 0.8364 (m) cc_final: 0.8073 (m) REVERT: M 200 THR cc_start: 0.8033 (m) cc_final: 0.7707 (p) REVERT: N 31 GLN cc_start: 0.6073 (tt0) cc_final: 0.5837 (tt0) REVERT: N 55 ILE cc_start: 0.8436 (mt) cc_final: 0.8103 (mm) REVERT: N 73 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7721 (mtmm) REVERT: N 155 LYS cc_start: 0.6859 (ptpt) cc_final: 0.6039 (tmtt) REVERT: O 9 ILE cc_start: 0.5793 (mp) cc_final: 0.5475 (mp) REVERT: O 160 VAL cc_start: 0.8578 (t) cc_final: 0.8223 (t) REVERT: O 199 THR cc_start: 0.7726 (p) cc_final: 0.7449 (t) REVERT: P 18 MET cc_start: 0.5297 (ttt) cc_final: 0.4562 (ttm) REVERT: P 66 SER cc_start: 0.7391 (m) cc_final: 0.6669 (t) REVERT: P 140 GLN cc_start: 0.6617 (tt0) cc_final: 0.5802 (mm110) REVERT: P 172 PHE cc_start: 0.7058 (m-10) cc_final: 0.6162 (m-80) outliers start: 47 outliers final: 25 residues processed: 1126 average time/residue: 0.1591 time to fit residues: 288.1946 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 : 0.929 ------------------------------------------------------------------------------- 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: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.173958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.161657 restraints weight = 33303.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.164655 restraints weight = 20389.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.166608 restraints weight = 13560.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.168003 restraints weight = 9549.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.168861 restraints weight = 7108.390| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24884 Z= 0.219 Angle : 0.818 9.728 33904 Z= 0.437 Chirality : 0.056 0.383 4208 Planarity : 0.007 0.076 4320 Dihedral : 7.799 29.245 3456 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.92 % Favored : 83.08 % Rotamer: Outliers : 0.41 % Allowed : 7.44 % Favored : 92.15 % 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: -4.13 (0.13), residues: 3280 helix: -0.93 (0.18), residues: 704 sheet: -3.17 (0.17), residues: 576 loop : -3.48 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 93 TYR 0.017 0.002 TYR K 35 PHE 0.029 0.003 PHE C 198 TRP 0.022 0.005 TRP J 127 HIS 0.009 0.003 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00507 (24880) covalent geometry : angle 0.81791 (33904) hydrogen bonds : bond 0.06068 ( 793) hydrogen bonds : angle 7.01549 ( 2244) Misc. bond : bond 0.00613 ( 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 948 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 937 time to evaluate : 1.072 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: symmetry clash REVERT: A 11 THR cc_start: 0.9346 (p) cc_final: 0.9083 (m) REVERT: A 43 THR cc_start: 0.8984 (p) cc_final: 0.8509 (t) REVERT: A 110 THR cc_start: 0.7651 (p) cc_final: 0.7309 (t) REVERT: A 133 ASN cc_start: 0.8351 (m-40) cc_final: 0.7846 (m-40) REVERT: A 155 LYS cc_start: 0.8533 (ptpt) cc_final: 0.7835 (tptt) REVERT: A 174 LYS cc_start: 0.6900 (mptt) cc_final: 0.6664 (mmtp) REVERT: A 200 THR cc_start: 0.8536 (m) cc_final: 0.8230 (p) REVERT: B 43 THR cc_start: 0.8060 (p) cc_final: 0.7540 (m) REVERT: B 49 GLN cc_start: 0.7766 (mt0) cc_final: 0.7281 (mm-40) REVERT: B 73 LYS cc_start: 0.7846 (tttt) cc_final: 0.7638 (tttt) REVERT: B 97 SER cc_start: 0.8078 (p) cc_final: 0.7781 (p) REVERT: B 182 ILE cc_start: 0.9434 (tp) cc_final: 0.9009 (tt) REVERT: C 18 MET cc_start: 0.6361 (ttm) cc_final: 0.6155 (ttm) REVERT: C 48 THR cc_start: 0.7727 (p) cc_final: 0.7420 (p) REVERT: C 155 LYS cc_start: 0.8447 (ptpp) cc_final: 0.8003 (ptpp) REVERT: C 178 PRO cc_start: 0.9012 (Cg_exo) cc_final: 0.8744 (Cg_endo) REVERT: D 92 THR cc_start: 0.9552 (m) cc_final: 0.9043 (t) REVERT: D 108 GLU cc_start: 0.7565 (tp30) cc_final: 0.7014 (tp30) REVERT: D 132 THR cc_start: 0.8872 (m) cc_final: 0.8586 (m) REVERT: D 133 ASN cc_start: 0.8344 (m-40) cc_final: 0.7358 (m-40) REVERT: D 172 PHE cc_start: 0.8377 (m-80) cc_final: 0.8169 (m-80) REVERT: D 200 THR cc_start: 0.8712 (m) cc_final: 0.8248 (p) REVERT: E 105 LEU cc_start: 0.7893 (mm) cc_final: 0.7473 (mm) REVERT: E 110 THR cc_start: 0.8150 (p) cc_final: 0.7548 (t) REVERT: E 143 ASP cc_start: 0.7751 (t0) cc_final: 0.7506 (t0) REVERT: E 176 ILE cc_start: 0.8223 (pt) cc_final: 0.8015 (mt) REVERT: E 183 THR cc_start: 0.6932 (m) cc_final: 0.6722 (p) REVERT: E 185 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8247 (pttm) REVERT: E 186 VAL cc_start: 0.9249 (t) cc_final: 0.8879 (m) REVERT: E 200 THR cc_start: 0.8751 (m) cc_final: 0.8346 (p) REVERT: F 112 TYR cc_start: 0.7363 (m-80) cc_final: 0.7159 (m-80) REVERT: G 36 LEU cc_start: 0.8006 (mt) cc_final: 0.7773 (mt) REVERT: G 203 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8124 (m) REVERT: H 139 LEU cc_start: 0.8532 (pp) cc_final: 0.8248 (pp) REVERT: H 158 ILE cc_start: 0.9123 (mt) cc_final: 0.8892 (tt) REVERT: H 181 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8360 (tptt) REVERT: H 185 LYS cc_start: 0.8927 (ptmt) cc_final: 0.8671 (pttm) REVERT: H 200 THR cc_start: 0.8341 (m) cc_final: 0.7949 (p) REVERT: I 66 SER cc_start: 0.7791 (m) cc_final: 0.7337 (p) REVERT: I 110 THR cc_start: 0.7571 (p) cc_final: 0.7009 (t) REVERT: I 112 TYR cc_start: 0.8004 (m-80) cc_final: 0.7377 (m-80) REVERT: I 158 ILE cc_start: 0.9503 (mt) cc_final: 0.8965 (tp) REVERT: I 200 THR cc_start: 0.8542 (m) cc_final: 0.8227 (p) REVERT: J 18 MET cc_start: 0.6161 (ttt) cc_final: 0.4913 (ptp) REVERT: J 91 ASN cc_start: 0.7923 (m110) cc_final: 0.7457 (m-40) REVERT: J 93 ARG cc_start: 0.8628 (mpt90) cc_final: 0.7281 (mmt180) REVERT: K 210 GLU cc_start: 0.8642 (pm20) cc_final: 0.8073 (pm20) REVERT: L 56 LYS cc_start: 0.8743 (pttp) cc_final: 0.8414 (ptpp) REVERT: M 133 ASN cc_start: 0.8121 (m-40) cc_final: 0.7799 (m-40) REVERT: M 172 PHE cc_start: 0.8241 (m-80) cc_final: 0.6106 (t80) REVERT: M 182 ILE cc_start: 0.8961 (tp) cc_final: 0.8607 (tt) REVERT: M 200 THR cc_start: 0.8621 (m) cc_final: 0.8326 (p) REVERT: N 106 LYS cc_start: 0.8273 (ttpp) cc_final: 0.7940 (tttt) REVERT: N 112 TYR cc_start: 0.8019 (m-80) cc_final: 0.7756 (m-80) REVERT: O 98 ASN cc_start: 0.7904 (t0) cc_final: 0.7407 (t0) REVERT: P 18 MET cc_start: 0.6727 (ttt) cc_final: 0.6179 (ttm) REVERT: P 49 GLN cc_start: 0.7236 (mp10) cc_final: 0.6673 (mm-40) REVERT: P 66 SER cc_start: 0.6453 (m) cc_final: 0.5924 (t) REVERT: P 89 LEU cc_start: 0.8084 (mt) cc_final: 0.7819 (mt) REVERT: P 132 THR cc_start: 0.8332 (m) cc_final: 0.8070 (m) REVERT: P 140 GLN cc_start: 0.6394 (tt0) cc_final: 0.5413 (mm110) REVERT: P 190 PHE cc_start: 0.7004 (p90) cc_final: 0.6788 (p90) outliers start: 11 outliers final: 5 residues processed: 943 average time/residue: 0.1505 time to fit residues: 232.7235 Evaluate side-chains 817 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 811 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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: 5.9990 chunk 150 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 155 optimal weight: 0.3980 chunk 12 optimal weight: 9.9990 chunk 116 optimal weight: 0.0170 chunk 84 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** F 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.176263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.163936 restraints weight = 33056.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.166959 restraints weight = 20392.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.168952 restraints weight = 13511.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.170320 restraints weight = 9548.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.171175 restraints weight = 7096.467| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3044 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= 0.182 Angle : 0.764 10.141 33904 Z= 0.406 Chirality : 0.055 0.399 4208 Planarity : 0.006 0.063 4320 Dihedral : 7.324 29.249 3456 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.10 % Favored : 83.90 % Rotamer: Outliers : 0.26 % Allowed : 7.63 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.84 (0.13), residues: 3280 helix: -0.34 (0.19), residues: 704 sheet: -3.04 (0.17), residues: 576 loop : -3.42 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 93 TYR 0.021 0.002 TYR D 112 PHE 0.027 0.003 PHE C 198 TRP 0.025 0.004 TRP G 127 HIS 0.012 0.003 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00427 (24880) covalent geometry : angle 0.76437 (33904) hydrogen bonds : bond 0.05001 ( 793) hydrogen bonds : angle 6.44455 ( 2244) Misc. bond : bond 0.00284 ( 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 918 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 911 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.9029 (p) cc_final: 0.8600 (t) REVERT: A 110 THR cc_start: 0.7500 (p) cc_final: 0.7142 (t) REVERT: A 131 ASN cc_start: 0.6936 (m-40) cc_final: 0.6674 (m-40) REVERT: A 133 ASN cc_start: 0.8450 (m-40) cc_final: 0.7845 (m-40) REVERT: A 155 LYS cc_start: 0.8409 (ptpt) cc_final: 0.7851 (tptt) REVERT: A 174 LYS cc_start: 0.7063 (mptt) cc_final: 0.6797 (mmtp) REVERT: A 200 THR cc_start: 0.8546 (m) cc_final: 0.8270 (p) REVERT: B 43 THR cc_start: 0.8089 (p) cc_final: 0.7849 (m) REVERT: B 49 GLN cc_start: 0.7897 (mt0) cc_final: 0.7444 (mm-40) REVERT: C 178 PRO cc_start: 0.8983 (Cg_exo) cc_final: 0.8730 (Cg_endo) REVERT: D 92 THR cc_start: 0.9535 (m) cc_final: 0.9108 (t) REVERT: D 108 GLU cc_start: 0.7376 (tp30) cc_final: 0.6880 (tp30) REVERT: D 132 THR cc_start: 0.8875 (m) cc_final: 0.8463 (m) REVERT: D 133 ASN cc_start: 0.8205 (m-40) cc_final: 0.7091 (m-40) REVERT: D 200 THR cc_start: 0.8749 (m) cc_final: 0.8147 (p) REVERT: E 105 LEU cc_start: 0.7917 (mm) cc_final: 0.7636 (mm) REVERT: E 110 THR cc_start: 0.8113 (p) cc_final: 0.7496 (t) REVERT: E 179 ARG cc_start: 0.7729 (ptp-110) cc_final: 0.7297 (mtm110) REVERT: E 186 VAL cc_start: 0.9187 (t) cc_final: 0.8975 (m) REVERT: E 200 THR cc_start: 0.8675 (m) cc_final: 0.8445 (p) REVERT: F 112 TYR cc_start: 0.7384 (m-80) cc_final: 0.6579 (m-10) REVERT: G 36 LEU cc_start: 0.7921 (mt) cc_final: 0.7709 (mt) REVERT: H 55 ILE cc_start: 0.9069 (mt) cc_final: 0.8823 (mm) REVERT: H 139 LEU cc_start: 0.8395 (pp) cc_final: 0.8166 (pp) REVERT: H 181 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8245 (tptt) REVERT: H 185 LYS cc_start: 0.8851 (ptmt) cc_final: 0.8631 (pttm) REVERT: H 200 THR cc_start: 0.8270 (m) cc_final: 0.7859 (p) REVERT: I 37 GLN cc_start: 0.7286 (tm-30) cc_final: 0.7033 (tm-30) REVERT: I 66 SER cc_start: 0.7491 (m) cc_final: 0.7135 (p) REVERT: I 110 THR cc_start: 0.7589 (p) cc_final: 0.7045 (t) REVERT: I 112 TYR cc_start: 0.8166 (m-80) cc_final: 0.7654 (m-80) REVERT: I 158 ILE cc_start: 0.9516 (mt) cc_final: 0.8991 (tp) REVERT: I 182 ILE cc_start: 0.9165 (tp) cc_final: 0.8808 (tt) REVERT: I 200 THR cc_start: 0.8405 (m) cc_final: 0.8153 (p) REVERT: J 18 MET cc_start: 0.5602 (ttt) cc_final: 0.4623 (ptp) REVERT: J 91 ASN cc_start: 0.7901 (m110) cc_final: 0.7338 (m-40) REVERT: J 127 TRP cc_start: 0.7040 (m100) cc_final: 0.6570 (m100) REVERT: K 43 THR cc_start: 0.8207 (p) cc_final: 0.8007 (p) REVERT: L 98 ASN cc_start: 0.5262 (t0) cc_final: 0.4785 (t0) REVERT: L 183 THR cc_start: 0.8589 (m) cc_final: 0.8140 (p) REVERT: M 112 TYR cc_start: 0.8007 (m-80) cc_final: 0.7769 (m-80) REVERT: M 125 THR cc_start: 0.7749 (p) cc_final: 0.7547 (p) REVERT: M 133 ASN cc_start: 0.8049 (m-40) cc_final: 0.7732 (m-40) REVERT: M 172 PHE cc_start: 0.7950 (m-80) cc_final: 0.6042 (t80) REVERT: M 179 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7274 (ptp90) REVERT: M 182 ILE cc_start: 0.8932 (tp) cc_final: 0.8541 (tt) REVERT: N 48 THR cc_start: 0.7860 (p) cc_final: 0.7397 (t) REVERT: N 106 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7783 (tttt) REVERT: N 172 PHE cc_start: 0.7441 (m-80) cc_final: 0.5391 (t80) REVERT: O 98 ASN cc_start: 0.8125 (t0) cc_final: 0.7684 (t0) REVERT: O 197 GLU cc_start: 0.7767 (tt0) cc_final: 0.7432 (tt0) REVERT: P 18 MET cc_start: 0.6428 (ttt) cc_final: 0.5838 (ttm) REVERT: P 66 SER cc_start: 0.6309 (m) cc_final: 0.5788 (t) REVERT: P 79 SER cc_start: 0.9250 (t) cc_final: 0.8780 (p) REVERT: P 140 GLN cc_start: 0.6524 (tt0) cc_final: 0.5452 (mm110) REVERT: P 174 LYS cc_start: 0.6795 (mttp) cc_final: 0.5883 (mmtm) outliers start: 7 outliers final: 4 residues processed: 918 average time/residue: 0.1530 time to fit residues: 230.8240 Evaluate side-chains 787 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 783 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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: 0.0770 chunk 271 optimal weight: 0.0270 chunk 244 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 297 optimal weight: 0.0010 chunk 113 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.2206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 140 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 41 GLN E 133 ASN ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 HIS L 91 ASN M 102 GLN M 133 ASN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 149 ASN O 41 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.182471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.170304 restraints weight = 32422.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.173430 restraints weight = 19777.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.175482 restraints weight = 12880.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.176766 restraints weight = 8999.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.177770 restraints weight = 6689.021| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24884 Z= 0.146 Angle : 0.721 8.638 33904 Z= 0.380 Chirality : 0.054 0.417 4208 Planarity : 0.005 0.064 4320 Dihedral : 6.845 27.276 3456 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.06 % Favored : 84.94 % Rotamer: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.01 % 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: -3.59 (0.13), residues: 3280 helix: 0.07 (0.19), residues: 704 sheet: -2.90 (0.18), residues: 576 loop : -3.34 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 45 TYR 0.018 0.001 TYR M 35 PHE 0.025 0.003 PHE C 198 TRP 0.022 0.003 TRP E 127 HIS 0.016 0.003 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00332 (24880) covalent geometry : angle 0.72096 (33904) hydrogen bonds : bond 0.04280 ( 793) hydrogen bonds : angle 6.02861 ( 2244) Misc. bond : bond 0.00214 ( 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 886 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 882 time to evaluate : 0.911 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: A 43 THR cc_start: 0.9056 (p) cc_final: 0.8598 (t) REVERT: A 131 ASN cc_start: 0.6631 (m-40) cc_final: 0.6258 (m-40) REVERT: A 133 ASN cc_start: 0.8340 (m-40) cc_final: 0.7842 (m-40) REVERT: A 155 LYS cc_start: 0.8321 (ptpt) cc_final: 0.7838 (tptt) REVERT: A 174 LYS cc_start: 0.6908 (mptt) cc_final: 0.6517 (mmtp) REVERT: A 200 THR cc_start: 0.8478 (m) cc_final: 0.8202 (p) REVERT: B 49 GLN cc_start: 0.7835 (mt0) cc_final: 0.7398 (mm-40) REVERT: B 127 TRP cc_start: 0.8100 (m100) cc_final: 0.7697 (m100) REVERT: D 18 MET cc_start: 0.6788 (tmm) cc_final: 0.6485 (tmm) REVERT: D 92 THR cc_start: 0.9456 (m) cc_final: 0.9188 (t) REVERT: D 108 GLU cc_start: 0.7532 (tp30) cc_final: 0.7082 (tp30) REVERT: D 132 THR cc_start: 0.8721 (m) cc_final: 0.8429 (m) REVERT: D 133 ASN cc_start: 0.8217 (m-40) cc_final: 0.7055 (m-40) REVERT: D 200 THR cc_start: 0.8582 (m) cc_final: 0.8150 (p) REVERT: E 105 LEU cc_start: 0.7773 (mm) cc_final: 0.7471 (mm) REVERT: E 143 ASP cc_start: 0.7641 (t0) cc_final: 0.7438 (t0) REVERT: E 186 VAL cc_start: 0.9134 (t) cc_final: 0.8896 (m) REVERT: F 189 GLU cc_start: 0.7791 (tt0) cc_final: 0.7524 (tt0) REVERT: F 204 TYR cc_start: 0.7148 (p90) cc_final: 0.6306 (p90) REVERT: G 36 LEU cc_start: 0.7852 (mt) cc_final: 0.7604 (mt) REVERT: G 181 LYS cc_start: 0.8468 (tppp) cc_final: 0.7661 (tppt) REVERT: G 197 GLU cc_start: 0.6787 (tt0) cc_final: 0.6576 (tt0) REVERT: H 55 ILE cc_start: 0.9045 (mt) cc_final: 0.8775 (mm) REVERT: H 185 LYS cc_start: 0.8758 (ptmt) cc_final: 0.8518 (pttm) REVERT: H 200 THR cc_start: 0.8128 (m) cc_final: 0.7763 (p) REVERT: I 37 GLN cc_start: 0.7353 (tm-30) cc_final: 0.6963 (tm-30) REVERT: I 66 SER cc_start: 0.7515 (m) cc_final: 0.7217 (p) REVERT: I 110 THR cc_start: 0.7807 (p) cc_final: 0.7164 (t) REVERT: I 112 TYR cc_start: 0.8085 (m-80) cc_final: 0.7607 (m-80) REVERT: I 158 ILE cc_start: 0.9451 (mt) cc_final: 0.8919 (tp) REVERT: I 172 PHE cc_start: 0.6987 (m-80) cc_final: 0.6182 (t80) REVERT: I 200 THR cc_start: 0.8358 (m) cc_final: 0.8012 (p) REVERT: J 18 MET cc_start: 0.5828 (ttt) cc_final: 0.4714 (ptp) REVERT: J 91 ASN cc_start: 0.7812 (m110) cc_final: 0.7197 (m-40) REVERT: L 98 ASN cc_start: 0.5291 (t0) cc_final: 0.4783 (t0) REVERT: L 163 VAL cc_start: 0.9358 (t) cc_final: 0.9140 (m) REVERT: L 183 THR cc_start: 0.8481 (m) cc_final: 0.8185 (p) REVERT: M 18 MET cc_start: 0.6524 (tpp) cc_final: 0.6239 (mmt) REVERT: M 106 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7988 (tttt) REVERT: M 110 THR cc_start: 0.7632 (p) cc_final: 0.7332 (t) REVERT: M 133 ASN cc_start: 0.7835 (m110) cc_final: 0.7513 (m-40) REVERT: M 179 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7297 (ptp90) REVERT: N 48 THR cc_start: 0.7839 (p) cc_final: 0.7358 (t) REVERT: N 72 GLU cc_start: 0.7736 (pm20) cc_final: 0.7170 (pm20) REVERT: N 172 PHE cc_start: 0.7375 (m-80) cc_final: 0.5576 (t80) REVERT: O 72 GLU cc_start: 0.8272 (pt0) cc_final: 0.8021 (pt0) REVERT: O 98 ASN cc_start: 0.8020 (t0) cc_final: 0.7648 (t0) REVERT: P 18 MET cc_start: 0.6207 (ttt) cc_final: 0.5862 (mtm) REVERT: P 132 THR cc_start: 0.8184 (m) cc_final: 0.7756 (m) REVERT: P 133 ASN cc_start: 0.7479 (m110) cc_final: 0.6280 (m110) REVERT: P 140 GLN cc_start: 0.6262 (tt0) cc_final: 0.5472 (mm110) REVERT: P 174 LYS cc_start: 0.6447 (mttp) cc_final: 0.5607 (mmtm) outliers start: 4 outliers final: 1 residues processed: 884 average time/residue: 0.1461 time to fit residues: 214.6517 Evaluate side-chains 773 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 772 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 171 optimal weight: 0.0670 chunk 149 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 113 HIS C 133 ASN D 81 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 133 ASN F 81 ASN H 140 GLN I 81 ASN I 113 HIS K 91 ASN M 91 ASN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN O 41 GLN O 102 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 HIS P 133 ASN P 148 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.175663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.163429 restraints weight = 32911.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.166413 restraints weight = 20317.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.168314 restraints weight = 13609.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.169760 restraints weight = 9688.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.170659 restraints weight = 7198.468| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24884 Z= 0.217 Angle : 0.772 9.331 33904 Z= 0.409 Chirality : 0.056 0.444 4208 Planarity : 0.006 0.068 4320 Dihedral : 6.962 28.950 3456 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.83 % Favored : 83.17 % Rotamer: Outliers : 0.11 % Allowed : 5.39 % Favored : 94.49 % 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: -3.50 (0.13), residues: 3280 helix: 0.26 (0.19), residues: 704 sheet: -2.76 (0.18), residues: 576 loop : -3.36 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 179 TYR 0.026 0.002 TYR E 70 PHE 0.027 0.003 PHE J 198 TRP 0.022 0.004 TRP O 127 HIS 0.016 0.003 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00526 (24880) covalent geometry : angle 0.77169 (33904) hydrogen bonds : bond 0.04484 ( 793) hydrogen bonds : angle 6.06414 ( 2244) Misc. bond : bond 0.00203 ( 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 871 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 868 time to evaluate : 0.928 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 110 THR cc_start: 0.7527 (p) cc_final: 0.7177 (t) REVERT: A 131 ASN cc_start: 0.6529 (m-40) cc_final: 0.6092 (m-40) REVERT: A 155 LYS cc_start: 0.8395 (ptpt) cc_final: 0.7895 (tptt) REVERT: A 174 LYS cc_start: 0.7315 (mptt) cc_final: 0.6959 (mmtp) REVERT: A 200 THR cc_start: 0.8506 (m) cc_final: 0.8137 (p) REVERT: B 49 GLN cc_start: 0.7728 (mt0) cc_final: 0.7326 (mm-40) REVERT: B 127 TRP cc_start: 0.8516 (m100) cc_final: 0.8194 (m100) REVERT: C 155 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8162 (ptpp) REVERT: D 132 THR cc_start: 0.8847 (m) cc_final: 0.8456 (m) REVERT: D 172 PHE cc_start: 0.5973 (t80) cc_final: 0.5471 (t80) REVERT: D 200 THR cc_start: 0.8668 (m) cc_final: 0.8162 (p) REVERT: E 143 ASP cc_start: 0.7577 (t0) cc_final: 0.7377 (t0) REVERT: E 185 LYS cc_start: 0.8695 (ptmt) cc_final: 0.8222 (pttm) REVERT: E 186 VAL cc_start: 0.9172 (t) cc_final: 0.8826 (m) REVERT: E 200 THR cc_start: 0.8726 (m) cc_final: 0.8343 (p) REVERT: F 98 ASN cc_start: 0.6443 (t0) cc_final: 0.6024 (m-40) REVERT: G 107 TYR cc_start: 0.8279 (t80) cc_final: 0.7782 (t80) REVERT: G 136 ILE cc_start: 0.9036 (tp) cc_final: 0.8755 (tp) REVERT: G 200 THR cc_start: 0.8702 (m) cc_final: 0.8369 (p) REVERT: H 37 GLN cc_start: 0.7360 (tm-30) cc_final: 0.7141 (tm-30) REVERT: H 185 LYS cc_start: 0.8833 (ptmt) cc_final: 0.8451 (pttm) REVERT: H 200 THR cc_start: 0.8351 (m) cc_final: 0.7889 (p) REVERT: I 66 SER cc_start: 0.7754 (m) cc_final: 0.7448 (p) REVERT: I 110 THR cc_start: 0.7783 (p) cc_final: 0.7285 (t) REVERT: I 112 TYR cc_start: 0.8259 (m-80) cc_final: 0.7877 (m-80) REVERT: I 158 ILE cc_start: 0.9495 (mt) cc_final: 0.9015 (mm) REVERT: I 172 PHE cc_start: 0.7195 (m-80) cc_final: 0.6214 (t80) REVERT: I 200 THR cc_start: 0.8476 (m) cc_final: 0.8149 (p) REVERT: J 18 MET cc_start: 0.5594 (ttt) cc_final: 0.4765 (mtm) REVERT: J 72 GLU cc_start: 0.6859 (pm20) cc_final: 0.6574 (pm20) REVERT: J 91 ASN cc_start: 0.7790 (m110) cc_final: 0.7363 (m-40) REVERT: L 98 ASN cc_start: 0.5094 (t0) cc_final: 0.4733 (t0) REVERT: L 183 THR cc_start: 0.8709 (m) cc_final: 0.8351 (p) REVERT: M 73 LYS cc_start: 0.8315 (mttt) cc_final: 0.8011 (mtmm) REVERT: M 106 LYS cc_start: 0.8331 (ttpp) cc_final: 0.8083 (tttt) REVERT: M 133 ASN cc_start: 0.8093 (m110) cc_final: 0.7833 (m-40) REVERT: M 179 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7337 (ptp90) REVERT: N 18 MET cc_start: 0.7844 (mtm) cc_final: 0.7453 (mtm) REVERT: N 48 THR cc_start: 0.7995 (p) cc_final: 0.7476 (t) REVERT: N 72 GLU cc_start: 0.7902 (pm20) cc_final: 0.7288 (pm20) REVERT: N 172 PHE cc_start: 0.7536 (m-80) cc_final: 0.5661 (t80) REVERT: O 46 GLU cc_start: 0.8557 (pm20) cc_final: 0.8154 (pm20) REVERT: O 98 ASN cc_start: 0.8075 (t0) cc_final: 0.7698 (t0) REVERT: O 131 ASN cc_start: 0.8130 (p0) cc_final: 0.7887 (p0) REVERT: O 202 SER cc_start: 0.7594 (m) cc_final: 0.7039 (m) REVERT: P 18 MET cc_start: 0.6224 (ttt) cc_final: 0.5675 (mtm) REVERT: P 69 THR cc_start: 0.7751 (m) cc_final: 0.7401 (m) REVERT: P 140 GLN cc_start: 0.6681 (tt0) cc_final: 0.5514 (mm110) outliers start: 3 outliers final: 1 residues processed: 870 average time/residue: 0.1510 time to fit residues: 217.3408 Evaluate side-chains 770 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 769 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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: 5.9990 chunk 146 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 309 optimal weight: 0.1980 chunk 16 optimal weight: 0.0020 chunk 262 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN E 41 GLN E 133 ASN ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 GLN I 148 GLN J 133 ASN L 31 GLN L 91 ASN M 91 ASN M 149 ASN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN O 41 GLN ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.186434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.174361 restraints weight = 32119.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.177513 restraints weight = 19387.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.179550 restraints weight = 12647.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.180985 restraints weight = 8780.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.181777 restraints weight = 6381.958| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24884 Z= 0.140 Angle : 0.718 9.802 33904 Z= 0.376 Chirality : 0.054 0.416 4208 Planarity : 0.005 0.069 4320 Dihedral : 6.606 27.269 3456 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.84 % Favored : 86.16 % Rotamer: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % 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: -3.30 (0.13), residues: 3280 helix: 0.39 (0.19), residues: 736 sheet: -2.37 (0.18), residues: 672 loop : -3.38 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 179 TYR 0.021 0.001 TYR B 204 PHE 0.029 0.002 PHE M 172 TRP 0.036 0.003 TRP K 127 HIS 0.013 0.002 HIS I 113 Details of bonding type rmsd covalent geometry : bond 0.00319 (24880) covalent geometry : angle 0.71816 (33904) hydrogen bonds : bond 0.03992 ( 793) hydrogen bonds : angle 5.84783 ( 2244) Misc. bond : bond 0.00167 ( 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 865 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 864 time to evaluate : 0.864 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: symmetry clash REVERT: A 155 LYS cc_start: 0.8463 (ptpt) cc_final: 0.7906 (tptt) REVERT: A 174 LYS cc_start: 0.6924 (mptt) cc_final: 0.6472 (mmtp) REVERT: A 200 THR cc_start: 0.8487 (m) cc_final: 0.8148 (p) REVERT: B 49 GLN cc_start: 0.7298 (mt0) cc_final: 0.6901 (mm-40) REVERT: B 202 SER cc_start: 0.7947 (m) cc_final: 0.7726 (m) REVERT: C 155 LYS cc_start: 0.8459 (ptpp) cc_final: 0.8094 (ptpp) REVERT: D 132 THR cc_start: 0.8755 (m) cc_final: 0.8408 (m) REVERT: D 200 THR cc_start: 0.8563 (m) cc_final: 0.8072 (p) REVERT: E 105 LEU cc_start: 0.7567 (mm) cc_final: 0.7339 (mm) REVERT: E 143 ASP cc_start: 0.7675 (t0) cc_final: 0.7403 (t0) REVERT: E 185 LYS cc_start: 0.8587 (ptmt) cc_final: 0.8085 (pttm) REVERT: E 186 VAL cc_start: 0.9045 (t) cc_final: 0.8720 (m) REVERT: G 113 HIS cc_start: 0.6660 (t70) cc_final: 0.6439 (t70) REVERT: G 144 ASN cc_start: 0.8185 (m-40) cc_final: 0.7902 (m110) REVERT: G 200 THR cc_start: 0.8727 (m) cc_final: 0.8430 (p) REVERT: H 185 LYS cc_start: 0.8672 (ptmt) cc_final: 0.8415 (pttm) REVERT: H 200 THR cc_start: 0.7986 (m) cc_final: 0.7585 (p) REVERT: I 64 THR cc_start: 0.7838 (t) cc_final: 0.7599 (t) REVERT: I 66 SER cc_start: 0.7643 (m) cc_final: 0.7370 (p) REVERT: I 110 THR cc_start: 0.7854 (p) cc_final: 0.7287 (t) REVERT: I 112 TYR cc_start: 0.8106 (m-80) cc_final: 0.7717 (m-80) REVERT: I 158 ILE cc_start: 0.9456 (mt) cc_final: 0.8905 (tp) REVERT: I 172 PHE cc_start: 0.6834 (m-80) cc_final: 0.6148 (t80) REVERT: I 200 THR cc_start: 0.8329 (m) cc_final: 0.7971 (p) REVERT: I 204 TYR cc_start: 0.6986 (p90) cc_final: 0.6410 (p90) REVERT: J 18 MET cc_start: 0.5652 (ttt) cc_final: 0.4803 (mtm) REVERT: J 108 GLU cc_start: 0.6153 (tm-30) cc_final: 0.5945 (tm-30) REVERT: K 43 THR cc_start: 0.8054 (p) cc_final: 0.7851 (p) REVERT: L 183 THR cc_start: 0.8639 (m) cc_final: 0.8321 (p) REVERT: M 18 MET cc_start: 0.6402 (tpp) cc_final: 0.6032 (mmt) REVERT: M 106 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7968 (tttt) REVERT: M 110 THR cc_start: 0.7510 (p) cc_final: 0.7157 (t) REVERT: M 127 TRP cc_start: 0.7766 (m100) cc_final: 0.7535 (m100) REVERT: M 133 ASN cc_start: 0.7889 (m110) cc_final: 0.7215 (m-40) REVERT: M 172 PHE cc_start: 0.6777 (m-10) cc_final: 0.6407 (t80) REVERT: N 48 THR cc_start: 0.7847 (p) cc_final: 0.7481 (t) REVERT: N 72 GLU cc_start: 0.7673 (pm20) cc_final: 0.7167 (pm20) REVERT: N 172 PHE cc_start: 0.7364 (m-80) cc_final: 0.5842 (t80) REVERT: O 98 ASN cc_start: 0.8060 (t0) cc_final: 0.7693 (t0) REVERT: O 112 TYR cc_start: 0.8006 (m-80) cc_final: 0.7799 (m-10) REVERT: O 131 ASN cc_start: 0.8022 (p0) cc_final: 0.7247 (p0) REVERT: P 18 MET cc_start: 0.5971 (ttt) cc_final: 0.5125 (mtp) REVERT: P 69 THR cc_start: 0.7697 (m) cc_final: 0.7489 (m) REVERT: P 108 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7449 (mm-30) REVERT: P 140 GLN cc_start: 0.6515 (tt0) cc_final: 0.5579 (mm110) REVERT: P 172 PHE cc_start: 0.7156 (m-80) cc_final: 0.5105 (t80) outliers start: 1 outliers final: 1 residues processed: 865 average time/residue: 0.1453 time to fit residues: 209.8853 Evaluate side-chains 761 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 760 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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: 1.9990 chunk 87 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 305 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 303 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN B 49 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 41 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN H 37 GLN K 91 ASN L 31 GLN ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 HIS M 149 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.183301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.174097 restraints weight = 32366.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.176310 restraints weight = 21231.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.177666 restraints weight = 14791.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.178694 restraints weight = 10838.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.179262 restraints weight = 8398.723| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24884 Z= 0.157 Angle : 0.723 9.912 33904 Z= 0.380 Chirality : 0.055 0.439 4208 Planarity : 0.006 0.073 4320 Dihedral : 6.513 27.849 3456 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.43 % Favored : 84.57 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: -3.22 (0.14), residues: 3280 helix: 0.49 (0.19), residues: 736 sheet: -2.27 (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 M 179 TYR 0.040 0.002 TYR P 70 PHE 0.021 0.002 PHE M 172 TRP 0.021 0.003 TRP K 127 HIS 0.013 0.003 HIS I 113 Details of bonding type rmsd covalent geometry : bond 0.00373 (24880) covalent geometry : angle 0.72296 (33904) hydrogen bonds : bond 0.04003 ( 793) hydrogen bonds : angle 5.77178 ( 2244) Misc. bond : bond 0.00741 ( 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 858 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 858 time to evaluate : 0.989 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 155 LYS cc_start: 0.8496 (ptpt) cc_final: 0.7953 (tptt) REVERT: A 174 LYS cc_start: 0.6997 (mptt) cc_final: 0.6573 (mmtp) REVERT: A 200 THR cc_start: 0.8420 (m) cc_final: 0.8059 (p) REVERT: C 155 LYS cc_start: 0.8484 (ptpp) cc_final: 0.8124 (ptpp) REVERT: D 92 THR cc_start: 0.9339 (m) cc_final: 0.8984 (p) REVERT: D 132 THR cc_start: 0.8617 (m) cc_final: 0.8414 (m) REVERT: D 200 THR cc_start: 0.8513 (m) cc_final: 0.8043 (p) REVERT: E 185 LYS cc_start: 0.8614 (ptmt) cc_final: 0.8122 (pttm) REVERT: E 186 VAL cc_start: 0.9038 (t) cc_final: 0.8706 (m) REVERT: F 132 THR cc_start: 0.8060 (p) cc_final: 0.7843 (p) REVERT: G 107 TYR cc_start: 0.8085 (t80) cc_final: 0.7633 (t80) REVERT: G 136 ILE cc_start: 0.9015 (tp) cc_final: 0.8670 (tp) REVERT: G 144 ASN cc_start: 0.8215 (m-40) cc_final: 0.7932 (m110) REVERT: G 200 THR cc_start: 0.8721 (m) cc_final: 0.8378 (p) REVERT: H 185 LYS cc_start: 0.8707 (ptmt) cc_final: 0.8372 (pttm) REVERT: H 200 THR cc_start: 0.8236 (m) cc_final: 0.7782 (p) REVERT: I 64 THR cc_start: 0.8049 (t) cc_final: 0.7821 (t) REVERT: I 66 SER cc_start: 0.7643 (m) cc_final: 0.7374 (p) REVERT: I 110 THR cc_start: 0.7951 (p) cc_final: 0.7387 (t) REVERT: I 112 TYR cc_start: 0.8255 (m-80) cc_final: 0.7784 (m-80) REVERT: I 158 ILE cc_start: 0.9487 (mt) cc_final: 0.9031 (mm) REVERT: I 172 PHE cc_start: 0.6912 (m-80) cc_final: 0.6143 (t80) REVERT: I 200 THR cc_start: 0.8357 (m) cc_final: 0.8017 (p) REVERT: I 204 TYR cc_start: 0.7087 (p90) cc_final: 0.6510 (p90) REVERT: J 18 MET cc_start: 0.5692 (ttt) cc_final: 0.4838 (mtm) REVERT: J 108 GLU cc_start: 0.6304 (tm-30) cc_final: 0.6066 (tm-30) REVERT: K 43 THR cc_start: 0.8152 (p) cc_final: 0.7922 (p) REVERT: K 49 GLN cc_start: 0.7609 (mt0) cc_final: 0.6938 (mt0) REVERT: L 109 LYS cc_start: 0.8322 (mppt) cc_final: 0.8023 (mppt) REVERT: L 179 ARG cc_start: 0.7275 (mtt-85) cc_final: 0.7071 (mtt-85) REVERT: L 183 THR cc_start: 0.8678 (m) cc_final: 0.8335 (p) REVERT: M 18 MET cc_start: 0.6489 (tpp) cc_final: 0.5990 (mmt) REVERT: M 106 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7983 (tttt) REVERT: M 110 THR cc_start: 0.7629 (p) cc_final: 0.7227 (t) REVERT: M 127 TRP cc_start: 0.7814 (m100) cc_final: 0.7596 (m100) REVERT: M 133 ASN cc_start: 0.7886 (m110) cc_final: 0.7197 (m-40) REVERT: M 172 PHE cc_start: 0.7130 (m-10) cc_final: 0.6397 (t80) REVERT: M 179 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7106 (ptp90) REVERT: N 48 THR cc_start: 0.7943 (p) cc_final: 0.7530 (t) REVERT: N 72 GLU cc_start: 0.7735 (pm20) cc_final: 0.7242 (pm20) REVERT: N 112 TYR cc_start: 0.7220 (m-80) cc_final: 0.6807 (m-80) REVERT: N 172 PHE cc_start: 0.7420 (m-80) cc_final: 0.5792 (t80) REVERT: O 98 ASN cc_start: 0.8002 (t0) cc_final: 0.7799 (t0) REVERT: O 179 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7531 (ttm-80) REVERT: O 202 SER cc_start: 0.7425 (m) cc_final: 0.5922 (m) REVERT: P 18 MET cc_start: 0.5946 (ttt) cc_final: 0.5128 (mtp) REVERT: P 112 TYR cc_start: 0.8174 (m-80) cc_final: 0.7917 (m-80) REVERT: P 140 GLN cc_start: 0.6472 (tt0) cc_final: 0.5397 (mm110) REVERT: P 172 PHE cc_start: 0.7227 (m-80) cc_final: 0.5307 (t80) outliers start: 0 outliers final: 0 residues processed: 858 average time/residue: 0.1499 time to fit residues: 212.8154 Evaluate side-chains 761 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 761 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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: 5.9990 chunk 295 optimal weight: 0.0470 chunk 256 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 126 optimal weight: 0.0000 chunk 101 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 overall best weight: 1.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN E 41 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN L 31 GLN L 91 ASN M 41 GLN M 91 ASN M 131 ASN M 149 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN O 102 GLN ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.188631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.179585 restraints weight = 31935.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.181841 restraints weight = 21033.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.183254 restraints weight = 14604.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.184214 restraints weight = 10719.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.184967 restraints weight = 8240.772| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24884 Z= 0.140 Angle : 0.720 9.744 33904 Z= 0.376 Chirality : 0.054 0.428 4208 Planarity : 0.006 0.075 4320 Dihedral : 6.354 26.187 3456 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.09 % Favored : 85.91 % Rotamer: Outliers : 0.04 % Allowed : 1.93 % Favored : 98.03 % 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: -3.09 (0.14), residues: 3280 helix: 0.66 (0.19), residues: 736 sheet: -2.15 (0.18), residues: 672 loop : -3.34 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 179 TYR 0.028 0.001 TYR L 35 PHE 0.025 0.002 PHE N 134 TRP 0.031 0.003 TRP D 127 HIS 0.016 0.002 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00321 (24880) covalent geometry : angle 0.71966 (33904) hydrogen bonds : bond 0.03795 ( 793) hydrogen bonds : angle 5.68982 ( 2244) Misc. bond : bond 0.00377 ( 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 849 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 848 time to evaluate : 0.939 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 155 LYS cc_start: 0.8464 (ptpt) cc_final: 0.7850 (tptt) REVERT: A 174 LYS cc_start: 0.6907 (mptt) cc_final: 0.6475 (mmtp) REVERT: A 200 THR cc_start: 0.8445 (m) cc_final: 0.8068 (p) REVERT: B 200 THR cc_start: 0.8663 (m) cc_final: 0.8103 (p) REVERT: B 202 SER cc_start: 0.8011 (m) cc_final: 0.7763 (m) REVERT: C 155 LYS cc_start: 0.8371 (ptpp) cc_final: 0.8068 (ptpp) REVERT: C 198 PHE cc_start: 0.8797 (p90) cc_final: 0.8558 (p90) REVERT: D 92 THR cc_start: 0.9332 (m) cc_final: 0.9040 (p) REVERT: D 132 THR cc_start: 0.8727 (m) cc_final: 0.8513 (m) REVERT: D 200 THR cc_start: 0.8397 (m) cc_final: 0.7965 (p) REVERT: E 105 LEU cc_start: 0.7444 (mm) cc_final: 0.7194 (mm) REVERT: E 143 ASP cc_start: 0.7698 (t0) cc_final: 0.7452 (t0) REVERT: E 179 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7118 (ttm-80) REVERT: E 185 LYS cc_start: 0.8580 (ptmt) cc_final: 0.8090 (pttm) REVERT: E 186 VAL cc_start: 0.9003 (t) cc_final: 0.8725 (m) REVERT: G 144 ASN cc_start: 0.7915 (m-40) cc_final: 0.7702 (m110) REVERT: G 200 THR cc_start: 0.8665 (m) cc_final: 0.8325 (p) REVERT: H 185 LYS cc_start: 0.8610 (ptmt) cc_final: 0.8316 (pttm) REVERT: H 200 THR cc_start: 0.8070 (m) cc_final: 0.7673 (p) REVERT: I 110 THR cc_start: 0.7755 (p) cc_final: 0.7196 (t) REVERT: I 112 TYR cc_start: 0.8272 (m-80) cc_final: 0.7954 (m-80) REVERT: I 158 ILE cc_start: 0.9481 (mt) cc_final: 0.9074 (mm) REVERT: I 172 PHE cc_start: 0.6783 (m-80) cc_final: 0.6048 (t80) REVERT: I 200 THR cc_start: 0.8227 (m) cc_final: 0.7861 (p) REVERT: I 204 TYR cc_start: 0.7020 (p90) cc_final: 0.6516 (p90) REVERT: J 18 MET cc_start: 0.5486 (ttt) cc_final: 0.4808 (mtm) REVERT: J 89 LEU cc_start: 0.8830 (mm) cc_final: 0.8600 (mm) REVERT: J 108 GLU cc_start: 0.6256 (tm-30) cc_final: 0.5967 (tm-30) REVERT: L 179 ARG cc_start: 0.7091 (mtt-85) cc_final: 0.6876 (mtt-85) REVERT: L 183 THR cc_start: 0.8645 (m) cc_final: 0.8350 (p) REVERT: M 18 MET cc_start: 0.6461 (tpp) cc_final: 0.6020 (mmt) REVERT: M 106 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7869 (tttt) REVERT: M 110 THR cc_start: 0.7386 (p) cc_final: 0.6917 (t) REVERT: M 127 TRP cc_start: 0.7741 (m100) cc_final: 0.7467 (m100) REVERT: M 179 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7130 (ptp90) REVERT: N 48 THR cc_start: 0.7832 (p) cc_final: 0.7422 (t) REVERT: N 72 GLU cc_start: 0.7570 (pm20) cc_final: 0.7067 (pm20) REVERT: N 112 TYR cc_start: 0.7151 (m-80) cc_final: 0.6806 (m-80) REVERT: N 172 PHE cc_start: 0.7321 (m-80) cc_final: 0.5760 (t80) REVERT: O 179 ARG cc_start: 0.7821 (ttm110) cc_final: 0.7535 (ttp-110) REVERT: O 202 SER cc_start: 0.7294 (m) cc_final: 0.5962 (m) REVERT: P 18 MET cc_start: 0.6201 (ttt) cc_final: 0.5161 (mtp) REVERT: P 66 SER cc_start: 0.6143 (m) cc_final: 0.5742 (t) REVERT: P 112 TYR cc_start: 0.8172 (m-80) cc_final: 0.7955 (m-80) REVERT: P 140 GLN cc_start: 0.6706 (tt0) cc_final: 0.5673 (mm110) REVERT: P 172 PHE cc_start: 0.7260 (m-80) cc_final: 0.5460 (t80) REVERT: P 181 LYS cc_start: 0.7381 (tppt) cc_final: 0.6882 (tptm) outliers start: 1 outliers final: 1 residues processed: 849 average time/residue: 0.1477 time to fit residues: 208.7929 Evaluate side-chains 740 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 739 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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: 0.0770 chunk 114 optimal weight: 0.0040 chunk 130 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 307 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 219 optimal weight: 0.8980 chunk 313 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.5954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN D 98 ASN E 41 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN L 31 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN M 149 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN ** O 148 GLN ** 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 = 0.3958 r_free = 0.3958 target = 0.187140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.178232 restraints weight = 32237.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.180418 restraints weight = 21122.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.181876 restraints weight = 14646.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.182751 restraints weight = 10650.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.183517 restraints weight = 8205.447| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24884 Z= 0.151 Angle : 0.729 10.262 33904 Z= 0.382 Chirality : 0.055 0.436 4208 Planarity : 0.006 0.078 4320 Dihedral : 6.346 25.716 3456 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.49 % Favored : 84.51 % Rotamer: Outliers : 0.07 % Allowed : 0.67 % Favored : 99.26 % 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: -3.05 (0.14), residues: 3280 helix: 0.71 (0.19), residues: 736 sheet: -2.06 (0.18), residues: 672 loop : -3.34 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 93 TYR 0.029 0.002 TYR L 35 PHE 0.026 0.002 PHE N 121 TRP 0.028 0.003 TRP C 127 HIS 0.010 0.002 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00360 (24880) covalent geometry : angle 0.72859 (33904) hydrogen bonds : bond 0.03830 ( 793) hydrogen bonds : angle 5.69428 ( 2244) Misc. bond : bond 0.00465 ( 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 831 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 829 time to evaluate : 0.918 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 155 LYS cc_start: 0.8528 (ptpt) cc_final: 0.7953 (tptt) REVERT: A 174 LYS cc_start: 0.6936 (mptt) cc_final: 0.6513 (mmtp) REVERT: A 200 THR cc_start: 0.8433 (m) cc_final: 0.8075 (p) REVERT: B 18 MET cc_start: 0.6562 (tpp) cc_final: 0.6331 (mmt) REVERT: B 200 THR cc_start: 0.8691 (m) cc_final: 0.8143 (p) REVERT: B 202 SER cc_start: 0.7984 (m) cc_final: 0.7782 (m) REVERT: C 33 SER cc_start: 0.8422 (m) cc_final: 0.8068 (p) REVERT: C 155 LYS cc_start: 0.8393 (ptpp) cc_final: 0.8192 (ptpp) REVERT: D 31 GLN cc_start: 0.7727 (tt0) cc_final: 0.7490 (tt0) REVERT: D 92 THR cc_start: 0.9387 (m) cc_final: 0.8897 (t) REVERT: E 129 LEU cc_start: 0.7850 (pt) cc_final: 0.7598 (pp) REVERT: E 143 ASP cc_start: 0.7561 (t0) cc_final: 0.7187 (t0) REVERT: E 179 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7011 (ttm-80) REVERT: E 185 LYS cc_start: 0.8708 (ptmt) cc_final: 0.8171 (pttm) REVERT: E 186 VAL cc_start: 0.9027 (t) cc_final: 0.8771 (m) REVERT: G 144 ASN cc_start: 0.8128 (m-40) cc_final: 0.7905 (m110) REVERT: G 188 PRO cc_start: 0.8175 (Cg_exo) cc_final: 0.7973 (Cg_endo) REVERT: G 200 THR cc_start: 0.8589 (m) cc_final: 0.8279 (p) REVERT: H 185 LYS cc_start: 0.8659 (ptmt) cc_final: 0.8337 (pttm) REVERT: I 110 THR cc_start: 0.7791 (p) cc_final: 0.7206 (t) REVERT: I 112 TYR cc_start: 0.8404 (m-80) cc_final: 0.8202 (m-80) REVERT: I 158 ILE cc_start: 0.9491 (mt) cc_final: 0.9104 (mm) REVERT: I 172 PHE cc_start: 0.6858 (m-80) cc_final: 0.6072 (t80) REVERT: I 200 THR cc_start: 0.8242 (m) cc_final: 0.7879 (p) REVERT: I 204 TYR cc_start: 0.7130 (p90) cc_final: 0.6650 (p90) REVERT: J 18 MET cc_start: 0.5488 (ttt) cc_final: 0.4872 (mtm) REVERT: J 89 LEU cc_start: 0.8791 (mm) cc_final: 0.8590 (mm) REVERT: J 140 GLN cc_start: 0.6731 (tt0) cc_final: 0.6308 (mm-40) REVERT: K 43 THR cc_start: 0.8019 (p) cc_final: 0.7795 (p) REVERT: K 49 GLN cc_start: 0.7268 (mt0) cc_final: 0.6215 (mp10) REVERT: K 185 LYS cc_start: 0.8591 (ptmt) cc_final: 0.8179 (pttp) REVERT: L 179 ARG cc_start: 0.7199 (mtt-85) cc_final: 0.6975 (mtt-85) REVERT: L 183 THR cc_start: 0.8576 (m) cc_final: 0.8264 (p) REVERT: M 73 LYS cc_start: 0.7774 (mttt) cc_final: 0.7506 (mttp) REVERT: M 106 LYS cc_start: 0.8121 (ttpp) cc_final: 0.7860 (tttt) REVERT: M 110 THR cc_start: 0.7398 (p) cc_final: 0.6997 (t) REVERT: M 127 TRP cc_start: 0.7692 (m100) cc_final: 0.7465 (m100) REVERT: M 172 PHE cc_start: 0.7531 (m-10) cc_final: 0.6361 (t80) REVERT: M 179 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7198 (ptp90) REVERT: N 48 THR cc_start: 0.7849 (p) cc_final: 0.7366 (t) REVERT: N 72 GLU cc_start: 0.7650 (pm20) cc_final: 0.7115 (pm20) REVERT: N 172 PHE cc_start: 0.7291 (m-80) cc_final: 0.5772 (t80) REVERT: O 179 ARG cc_start: 0.7818 (ttm110) cc_final: 0.7585 (ttp-110) REVERT: O 198 PHE cc_start: 0.8615 (m-80) cc_final: 0.8377 (m-80) REVERT: O 202 SER cc_start: 0.7343 (m) cc_final: 0.6026 (m) REVERT: P 18 MET cc_start: 0.5968 (ttt) cc_final: 0.5007 (mtp) REVERT: P 66 SER cc_start: 0.6075 (m) cc_final: 0.5774 (t) REVERT: P 140 GLN cc_start: 0.6688 (tt0) cc_final: 0.5626 (mm110) REVERT: P 172 PHE cc_start: 0.7232 (m-80) cc_final: 0.5442 (t80) REVERT: P 174 LYS cc_start: 0.7515 (tmmt) cc_final: 0.7096 (tppt) outliers start: 2 outliers final: 1 residues processed: 831 average time/residue: 0.1445 time to fit residues: 200.4154 Evaluate side-chains 738 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 737 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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: 0.8980 chunk 286 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 220 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN C 212 GLN D 98 ASN E 41 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN K 149 ASN L 31 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 HIS ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN O 41 GLN O 102 GLN ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.188677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.176217 restraints weight = 31785.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.179458 restraints weight = 19196.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.181626 restraints weight = 12568.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.183113 restraints weight = 8668.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.184101 restraints weight = 6281.122| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24884 Z= 0.153 Angle : 0.732 10.203 33904 Z= 0.383 Chirality : 0.055 0.447 4208 Planarity : 0.006 0.081 4320 Dihedral : 6.322 25.534 3456 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.40 % Favored : 84.60 % Rotamer: Outliers : 0.07 % Allowed : 0.71 % Favored : 99.22 % 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: -3.04 (0.14), residues: 3280 helix: 0.74 (0.19), residues: 736 sheet: -2.03 (0.18), residues: 672 loop : -3.35 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 179 TYR 0.021 0.001 TYR J 35 PHE 0.040 0.003 PHE C 198 TRP 0.029 0.003 TRP D 127 HIS 0.015 0.003 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00365 (24880) covalent geometry : angle 0.73170 (33904) hydrogen bonds : bond 0.03774 ( 793) hydrogen bonds : angle 5.68431 ( 2244) Misc. bond : bond 0.00413 ( 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 805 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 803 time to evaluate : 1.063 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: 0.8529 (ptpt) cc_final: 0.7943 (tptt) REVERT: A 174 LYS cc_start: 0.6965 (mptt) cc_final: 0.6542 (mmtp) REVERT: A 200 THR cc_start: 0.8439 (m) cc_final: 0.8052 (p) REVERT: B 18 MET cc_start: 0.6683 (tpp) cc_final: 0.6476 (mmt) REVERT: B 200 THR cc_start: 0.8668 (m) cc_final: 0.8113 (p) REVERT: C 33 SER cc_start: 0.8421 (m) cc_final: 0.8091 (p) REVERT: C 155 LYS cc_start: 0.8421 (ptpp) cc_final: 0.8192 (ptpp) REVERT: C 178 PRO cc_start: 0.8924 (Cg_exo) cc_final: 0.8713 (Cg_endo) REVERT: D 91 ASN cc_start: 0.8419 (m-40) cc_final: 0.8039 (m-40) REVERT: D 92 THR cc_start: 0.9380 (m) cc_final: 0.8928 (t) REVERT: E 143 ASP cc_start: 0.7569 (t0) cc_final: 0.7253 (t0) REVERT: E 179 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7100 (ttm-80) REVERT: E 185 LYS cc_start: 0.8715 (ptmt) cc_final: 0.8163 (pttm) REVERT: E 186 VAL cc_start: 0.9020 (t) cc_final: 0.8756 (m) REVERT: F 32 THR cc_start: 0.8959 (p) cc_final: 0.8569 (t) REVERT: G 144 ASN cc_start: 0.8171 (m-40) cc_final: 0.7951 (m110) REVERT: G 200 THR cc_start: 0.8593 (m) cc_final: 0.8241 (p) REVERT: H 110 THR cc_start: 0.7480 (p) cc_final: 0.7104 (t) REVERT: H 127 TRP cc_start: 0.7911 (m100) cc_final: 0.7445 (m100) REVERT: H 185 LYS cc_start: 0.8675 (ptmt) cc_final: 0.8316 (pttm) REVERT: I 110 THR cc_start: 0.7778 (p) cc_final: 0.7113 (t) REVERT: I 112 TYR cc_start: 0.8454 (m-80) cc_final: 0.8007 (m-80) REVERT: I 158 ILE cc_start: 0.9518 (mt) cc_final: 0.9062 (mm) REVERT: I 172 PHE cc_start: 0.6926 (m-80) cc_final: 0.6077 (t80) REVERT: I 200 THR cc_start: 0.8145 (m) cc_final: 0.7777 (p) REVERT: I 204 TYR cc_start: 0.7094 (p90) cc_final: 0.6650 (p90) REVERT: J 18 MET cc_start: 0.5738 (ttt) cc_final: 0.4894 (mtp) REVERT: J 91 ASN cc_start: 0.7719 (m110) cc_final: 0.7372 (m-40) REVERT: J 140 GLN cc_start: 0.6796 (tt0) cc_final: 0.6244 (mm-40) REVERT: K 49 GLN cc_start: 0.7187 (mt0) cc_final: 0.6518 (mt0) REVERT: K 185 LYS cc_start: 0.8602 (ptmt) cc_final: 0.8167 (pttp) REVERT: L 179 ARG cc_start: 0.7237 (mtt-85) cc_final: 0.7003 (mtt-85) REVERT: L 183 THR cc_start: 0.8593 (m) cc_final: 0.8273 (p) REVERT: M 73 LYS cc_start: 0.7908 (mttt) cc_final: 0.7590 (mttp) REVERT: M 106 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7898 (tttt) REVERT: M 110 THR cc_start: 0.7437 (p) cc_final: 0.7001 (t) REVERT: M 179 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7194 (ptp90) REVERT: N 48 THR cc_start: 0.7995 (p) cc_final: 0.7472 (t) REVERT: N 72 GLU cc_start: 0.7649 (pm20) cc_final: 0.7377 (pm20) REVERT: N 172 PHE cc_start: 0.7335 (m-80) cc_final: 0.5748 (t80) REVERT: P 18 MET cc_start: 0.6057 (ttt) cc_final: 0.5031 (mtp) REVERT: P 66 SER cc_start: 0.6139 (m) cc_final: 0.5859 (t) REVERT: P 140 GLN cc_start: 0.6749 (tt0) cc_final: 0.5448 (mm110) REVERT: P 172 PHE cc_start: 0.7267 (m-80) cc_final: 0.5522 (t80) REVERT: P 174 LYS cc_start: 0.7499 (tmmt) cc_final: 0.6818 (tppt) REVERT: P 181 LYS cc_start: 0.7526 (tppt) cc_final: 0.6954 (tptm) REVERT: P 188 PRO cc_start: 0.9437 (Cg_endo) cc_final: 0.9083 (Cg_exo) outliers start: 2 outliers final: 1 residues processed: 805 average time/residue: 0.1461 time to fit residues: 196.9615 Evaluate side-chains 724 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 723 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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: 7.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 296 optimal weight: 0.0980 chunk 239 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 140 optimal weight: 0.0970 chunk 238 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 199 optimal weight: 0.0370 chunk 285 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN D 98 ASN D 102 GLN E 41 GLN E 133 ASN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN L 31 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 HIS O 41 GLN ** O 140 GLN ** 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 = 0.4014 r_free = 0.4014 target = 0.192699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.183495 restraints weight = 32025.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.185787 restraints weight = 20997.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.187130 restraints weight = 14607.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.188245 restraints weight = 10799.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.188857 restraints weight = 8256.904| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24884 Z= 0.137 Angle : 0.722 9.911 33904 Z= 0.376 Chirality : 0.053 0.398 4208 Planarity : 0.006 0.081 4320 Dihedral : 6.170 27.049 3456 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 0.04 % Allowed : 0.60 % Favored : 99.37 % 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: -2.94 (0.14), residues: 3280 helix: 0.82 (0.19), residues: 736 sheet: -1.70 (0.19), residues: 640 loop : -3.39 (0.12), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 179 TYR 0.022 0.001 TYR K 204 PHE 0.020 0.003 PHE M 172 TRP 0.029 0.003 TRP A 127 HIS 0.010 0.002 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00309 (24880) covalent geometry : angle 0.72188 (33904) hydrogen bonds : bond 0.03610 ( 793) hydrogen bonds : angle 5.61223 ( 2244) Misc. bond : bond 0.00353 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4671.83 seconds wall clock time: 81 minutes 43.37 seconds (4903.37 seconds total)