Starting phenix.real_space_refine (version: dev) on Sat Feb 25 03:29:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/02_2023/5o4u_3746.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/02_2023/5o4u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/02_2023/5o4u_3746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/02_2023/5o4u_3746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/02_2023/5o4u_3746.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/02_2023/5o4u_3746.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/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: 13.46, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.91 Conformation dependent library (CDL) restraints added in 3.7 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: 1.14 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: 6.73 Time building geometry restraints manager: 11.50 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: 99.15 - 106.11: 472 106.11 - 113.07: 13809 113.07 - 120.04: 8303 120.04 - 127.00: 11131 127.00 - 133.96: 189 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: 0.59 - 1.45: 5 1.45 - 2.31: 51 2.31 - 3.17: 21768 3.17 - 4.04: 61959 4.04 - 4.90: 109146 Warning: very small nonbonded interaction distances. Nonbonded interactions: 192929 Sorted by model distance: nonbonded pdb=" CA GLY K 34 " pdb=" NE2 GLN K 37 " model vdw 0.586 3.520 nonbonded pdb=" O GLY K 34 " pdb=" OE1 GLN K 37 " model vdw 0.830 3.040 nonbonded pdb=" C GLY K 34 " pdb=" NE2 GLN K 37 " model vdw 1.185 3.350 nonbonded pdb=" NZ LYS B 39 " pdb=" CG2 THR B 43 " model vdw 1.227 3.540 nonbonded pdb=" O GLY K 34 " pdb=" CD GLN K 37 " model vdw 1.291 3.270 ... (remaining 192924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 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. 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: 0.440 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: 4.180 Check model and map are aligned: 0.330 Process input model: 60.190 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 : 0.007 0.100 24880 Z= 0.455 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 : 0.586 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.26 % Favored : 82.74 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 47 poor density : 1105 time to evaluate : 2.648 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 outliers start: 47 outliers final: 25 residues processed: 1126 average time/residue: 0.3376 time to fit residues: 603.3114 Evaluate side-chains 831 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 806 time to evaluate : 2.761 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 2 residues processed: 25 average time/residue: 0.2196 time to fit residues: 13.9620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 5.9990 chunk 242 optimal weight: 0.0370 chunk 134 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 overall best weight: 2.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 GLN D 31 GLN D 91 ASN D 133 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 ASN E 133 ASN ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 GLN J 41 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN K 91 ASN ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 140 GLN M 31 GLN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 ASN M 133 ASN M 149 ASN N 31 GLN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 91 ASN N 149 ASN ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 GLN P 149 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 24880 Z= 0.259 Angle : 0.759 9.264 33904 Z= 0.403 Chirality : 0.054 0.312 4208 Planarity : 0.006 0.073 4320 Dihedral : 7.472 29.359 3456 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.55 % Favored : 84.45 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.13), residues: 3280 helix: -0.89 (0.18), residues: 704 sheet: -3.14 (0.17), residues: 576 loop : -3.47 (0.12), residues: 2000 *********************** 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 944 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 921 time to evaluate : 2.587 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 outliers start: 23 outliers final: 12 residues processed: 929 average time/residue: 0.3267 time to fit residues: 491.6788 Evaluate side-chains 777 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 765 time to evaluate : 2.889 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2255 time to fit residues: 9.3684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 80 optimal weight: 100.0000 chunk 291 optimal weight: 0.0270 chunk 314 optimal weight: 6.9990 chunk 259 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 233 optimal weight: 4.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 113 HIS A 133 ASN A 140 GLN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 91 ASN D 113 HIS ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN I 102 GLN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 ASN ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN L 49 GLN L 140 GLN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN M 133 ASN M 149 ASN N 31 GLN N 102 GLN ** N 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN O 41 GLN O 102 GLN P 41 GLN ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 24880 Z= 0.314 Angle : 0.767 9.546 33904 Z= 0.409 Chirality : 0.054 0.359 4208 Planarity : 0.006 0.064 4320 Dihedral : 7.262 28.371 3456 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.62 % Favored : 82.38 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.13), residues: 3280 helix: -0.19 (0.19), residues: 704 sheet: -2.63 (0.17), residues: 672 loop : -3.57 (0.12), residues: 1904 *********************** 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 893 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 871 time to evaluate : 2.688 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 outliers start: 22 outliers final: 13 residues processed: 881 average time/residue: 0.3314 time to fit residues: 475.9288 Evaluate side-chains 770 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 757 time to evaluate : 2.987 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2394 time to fit residues: 9.6829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 0.7980 chunk 218 optimal weight: 6.9990 chunk 151 optimal weight: 0.0970 chunk 32 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 292 optimal weight: 0.7980 chunk 309 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 276 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 49 GLN A 140 GLN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 GLN ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN K 149 ASN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN M 102 GLN M 133 ASN M 149 ASN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN ** N 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN O 41 GLN O 148 GLN ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 133 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 24880 Z= 0.214 Angle : 0.706 8.684 33904 Z= 0.373 Chirality : 0.052 0.312 4208 Planarity : 0.005 0.063 4320 Dihedral : 6.788 31.273 3456 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.54 % Favored : 85.46 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.13), residues: 3280 helix: 0.29 (0.19), residues: 704 sheet: -2.50 (0.17), residues: 672 loop : -3.47 (0.12), residues: 1904 *********************** 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 877 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 869 time to evaluate : 2.851 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 outliers start: 8 outliers final: 6 residues processed: 873 average time/residue: 0.3242 time to fit residues: 460.3296 Evaluate side-chains 742 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 736 time to evaluate : 2.622 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2118 time to fit residues: 6.1046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 263 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 277 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 102 GLN A 133 ASN ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS C 140 GLN ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 148 GLN E 31 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 133 ASN I 81 ASN K 91 ASN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 ASN ** L 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN M 98 ASN ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 GLN ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 24880 Z= 0.303 Angle : 0.747 9.059 33904 Z= 0.396 Chirality : 0.055 0.423 4208 Planarity : 0.006 0.077 4320 Dihedral : 6.853 29.134 3456 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.62 % Favored : 82.38 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.13), residues: 3280 helix: 0.35 (0.19), residues: 736 sheet: -2.44 (0.16), residues: 752 loop : -3.49 (0.13), residues: 1792 *********************** 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 844 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 840 time to evaluate : 2.991 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 outliers start: 4 outliers final: 1 residues processed: 843 average time/residue: 0.3364 time to fit residues: 462.4442 Evaluate side-chains 720 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 719 time to evaluate : 2.792 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2306 time to fit residues: 4.4847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 257 optimal weight: 0.5980 chunk 143 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 149 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN N 149 ASN O 41 GLN O 148 GLN ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 133 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 24880 Z= 0.213 Angle : 0.714 8.882 33904 Z= 0.375 Chirality : 0.054 0.415 4208 Planarity : 0.005 0.067 4320 Dihedral : 6.558 27.309 3456 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.14), residues: 3280 helix: 0.62 (0.19), residues: 736 sheet: -2.29 (0.17), residues: 752 loop : -3.42 (0.13), residues: 1792 *********************** 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 841 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 839 time to evaluate : 2.981 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 outliers start: 2 outliers final: 0 residues processed: 841 average time/residue: 0.3118 time to fit residues: 431.4810 Evaluate side-chains 724 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 724 time to evaluate : 2.770 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 260 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 308 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN C 113 HIS D 91 ASN D 133 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN L 140 GLN M 91 ASN M 98 ASN M 149 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 133 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24880 Z= 0.228 Angle : 0.710 8.296 33904 Z= 0.373 Chirality : 0.054 0.447 4208 Planarity : 0.006 0.076 4320 Dihedral : 6.444 27.850 3456 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.46 % Favored : 83.54 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.14), residues: 3280 helix: 0.81 (0.19), residues: 736 sheet: -2.09 (0.18), residues: 672 loop : -3.41 (0.12), residues: 1872 *********************** 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 815 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 814 time to evaluate : 2.959 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 outliers start: 1 outliers final: 0 residues processed: 815 average time/residue: 0.3273 time to fit residues: 438.1151 Evaluate side-chains 708 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 708 time to evaluate : 3.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 196 optimal weight: 0.1980 chunk 210 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN M 149 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 91 ASN O 41 GLN ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 ASN P 133 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 24880 Z= 0.225 Angle : 0.719 9.338 33904 Z= 0.378 Chirality : 0.055 0.491 4208 Planarity : 0.006 0.075 4320 Dihedral : 6.360 26.619 3456 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.46 % Favored : 84.54 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.14), residues: 3280 helix: 0.92 (0.19), residues: 736 sheet: -2.00 (0.18), residues: 672 loop : -3.41 (0.12), residues: 1872 *********************** 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 804 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 803 time to evaluate : 2.614 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 outliers start: 1 outliers final: 0 residues processed: 804 average time/residue: 0.3169 time to fit residues: 416.3944 Evaluate side-chains 695 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 695 time to evaluate : 2.771 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 chunk 269 optimal weight: 8.9990 chunk 287 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 259 optimal weight: 20.0000 chunk 271 optimal weight: 6.9990 chunk 286 optimal weight: 0.0980 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS D 91 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN M 98 ASN M 113 HIS ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 149 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN O 41 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 133 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 24880 Z= 0.352 Angle : 0.796 9.368 33904 Z= 0.422 Chirality : 0.059 0.540 4208 Planarity : 0.006 0.082 4320 Dihedral : 6.694 28.058 3456 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.20 % Favored : 81.80 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.14), residues: 3280 helix: 0.73 (0.19), residues: 736 sheet: -1.96 (0.19), residues: 672 loop : -3.49 (0.12), residues: 1872 *********************** 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 800 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 799 time to evaluate : 2.973 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 outliers start: 1 outliers final: 0 residues processed: 800 average time/residue: 0.3266 time to fit residues: 426.1452 Evaluate side-chains 698 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 698 time to evaluate : 2.952 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 10.0000 chunk 303 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 318 optimal weight: 0.9990 chunk 293 optimal weight: 0.3980 chunk 253 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN M 98 ASN M 113 HIS M 149 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN O 41 GLN P 133 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 24880 Z= 0.292 Angle : 0.782 9.454 33904 Z= 0.412 Chirality : 0.058 0.544 4208 Planarity : 0.006 0.083 4320 Dihedral : 6.721 29.673 3456 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.55 % Favored : 83.45 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.14), residues: 3280 helix: 0.80 (0.19), residues: 736 sheet: -1.97 (0.19), residues: 672 loop : -3.47 (0.12), residues: 1872 ********************** 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 793 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 791 time to evaluate : 2.726 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 outliers start: 2 outliers final: 0 residues processed: 793 average time/residue: 0.3188 time to fit residues: 413.8003 Evaluate side-chains 698 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 698 time to evaluate : 2.787 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 77 optimal weight: 0.0370 chunk 234 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 254 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.2862 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 38 GLN C 149 ASN D 49 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN L 31 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 149 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN P 133 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.181730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.170741 restraints weight = 32371.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.173354 restraints weight = 20471.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.174964 restraints weight = 13947.249| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 24880 Z= 0.278 Angle : 0.768 9.399 33904 Z= 0.404 Chirality : 0.057 0.487 4208 Planarity : 0.006 0.082 4320 Dihedral : 6.625 28.720 3456 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.32 % Favored : 82.68 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.14), residues: 3280 helix: 0.89 (0.19), residues: 736 sheet: -1.97 (0.19), residues: 672 loop : -3.46 (0.12), residues: 1872 =============================================================================== Job complete usr+sys time: 6853.35 seconds wall clock time: 125 minutes 10.19 seconds (7510.19 seconds total)