Starting phenix.real_space_refine on Sun Feb 25 11:03:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe1_12857/02_2024/7oe1_12857.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe1_12857/02_2024/7oe1_12857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe1_12857/02_2024/7oe1_12857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe1_12857/02_2024/7oe1_12857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe1_12857/02_2024/7oe1_12857.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe1_12857/02_2024/7oe1_12857.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1530 5.49 5 S 63 5.16 5 C 26069 2.51 5 N 9537 2.21 5 O 13893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 77": "OE1" <-> "OE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "O GLU 25": "OE1" <-> "OE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "N GLU 85": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51092 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 32831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1530, 32831 Classifications: {'RNA': 1530} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 82, 'rna3p_pur': 760, 'rna3p_pyr': 576} Link IDs: {'rna2p': 194, 'rna3p': 1335} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "U" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 148 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "G" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Time building chain proxies: 26.94, per 1000 atoms: 0.53 Number of scatterers: 51092 At special positions: 0 Unit cell: (141.9, 191.78, 240.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 1530 15.00 O 13893 8.00 N 9537 7.00 C 26069 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: 34.08 Conformation dependent library (CDL) restraints added in 4.2 seconds 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4298 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 21 sheets defined 41.2% alpha, 11.1% beta 503 base pairs and 795 stacking pairs defined. Time for finding SS restraints: 23.83 Creating SS restraints... Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.846A pdb=" N ARG D 13 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 65 removed outlier: 4.161A pdb=" N GLU D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.612A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 153 through 158 removed outlier: 3.545A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.937A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 69 removed outlier: 3.544A pdb=" N ARG E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 3.810A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 removed outlier: 4.250A pdb=" N ARG E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'F' and resid 11 through 16 removed outlier: 3.878A pdb=" N SER F 15 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 31 removed outlier: 4.132A pdb=" N ALA F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.876A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE F 80 " --> pdb=" O THR F 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 16 Processing helix chain 'H' and resid 30 through 42 removed outlier: 3.715A pdb=" N VAL H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 98 Processing helix chain 'H' and resid 111 through 118 Processing helix chain 'K' and resid 47 through 49 No H-bonds generated for 'chain 'K' and resid 47 through 49' Processing helix chain 'K' and resid 58 through 74 removed outlier: 3.645A pdb=" N ALA K 62 " --> pdb=" O THR K 58 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL K 64 " --> pdb=" O PHE K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 92 Processing helix chain 'K' and resid 93 through 102 removed outlier: 3.511A pdb=" N ARG K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 9 Processing helix chain 'L' and resid 112 through 116 Processing helix chain 'O' and resid 3 through 15 removed outlier: 3.731A pdb=" N ILE O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 43 removed outlier: 4.211A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 73 removed outlier: 3.789A pdb=" N ARG O 52 " --> pdb=" O ASP O 48 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG O 53 " --> pdb=" O HIS O 49 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR O 68 " --> pdb=" O LYS O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 84 removed outlier: 3.637A pdb=" N TYR O 77 " --> pdb=" O ASP O 73 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG O 83 " --> pdb=" O ARG O 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 removed outlier: 3.578A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 82 removed outlier: 3.662A pdb=" N ALA P 73 " --> pdb=" O ASP P 69 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 29 removed outlier: 3.956A pdb=" N LYS R 29 " --> pdb=" O ALA R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.654A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 5 through 31 removed outlier: 4.216A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR T 29 " --> pdb=" O SER T 25 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 39 removed outlier: 3.567A pdb=" N ALA T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 63 Proline residue: T 55 - end of helix removed outlier: 3.597A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA T 61 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS T 63 " --> pdb=" O ARG T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 84 removed outlier: 3.593A pdb=" N LEU T 78 " --> pdb=" O HIS T 74 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN T 81 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.703A pdb=" N GLU B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 52 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 removed outlier: 3.576A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 127 removed outlier: 3.530A pdb=" N SER B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 125 " --> pdb=" O GLN B 121 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 146 removed outlier: 4.600A pdb=" N LYS B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.628A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 221 removed outlier: 3.647A pdb=" N VAL B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'U' and resid 39 through 44 Processing helix chain 'U' and resid 46 through 51 removed outlier: 3.557A pdb=" N SER U 50 " --> pdb=" O ARG U 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.643A pdb=" N ILE C 9 " --> pdb=" O HIS C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.838A pdb=" N ASN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 removed outlier: 3.842A pdb=" N ALA C 47 " --> pdb=" O LYS C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.524A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 76' Processing helix chain 'C' and resid 80 through 94 removed outlier: 3.579A pdb=" N ARG C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 111 through 124 removed outlier: 3.611A pdb=" N GLU C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 143 removed outlier: 3.699A pdb=" N ALA C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN C 139 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 removed outlier: 3.508A pdb=" N PHE G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET G 30 " --> pdb=" O VAL G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 40 Processing helix chain 'G' and resid 42 through 54 removed outlier: 3.568A pdb=" N THR G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA G 50 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 63 removed outlier: 3.798A pdb=" N GLU G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 82 Processing helix chain 'G' and resid 91 through 96 removed outlier: 4.015A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 102 Processing helix chain 'G' and resid 114 through 123 removed outlier: 4.034A pdb=" N LEU G 119 " --> pdb=" O MET G 115 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU G 122 " --> pdb=" O ARG G 118 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU G 123 " --> pdb=" O LEU G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 144 removed outlier: 3.923A pdb=" N ASP G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL G 140 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS G 141 " --> pdb=" O ARG G 137 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG G 142 " --> pdb=" O GLU G 138 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET G 143 " --> pdb=" O ASP G 139 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 135 through 144' Processing helix chain 'I' and resid 33 through 38 Processing helix chain 'I' and resid 48 through 52 Processing helix chain 'I' and resid 56 through 58 No H-bonds generated for 'chain 'I' and resid 56 through 58' Processing helix chain 'I' and resid 72 through 80 removed outlier: 3.685A pdb=" N ILE I 78 " --> pdb=" O GLN I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 86 Processing helix chain 'I' and resid 93 through 101 removed outlier: 3.894A pdb=" N LEU I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 25 removed outlier: 5.555A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 30 Processing helix chain 'J' and resid 80 through 86 removed outlier: 3.621A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 89 No H-bonds generated for 'chain 'J' and resid 87 through 89' Processing helix chain 'M' and resid 13 through 19 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 43 through 47 Processing helix chain 'M' and resid 48 through 62 removed outlier: 3.590A pdb=" N ILE M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU M 55 " --> pdb=" O GLN M 51 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 80 removed outlier: 4.279A pdb=" N ARG M 69 " --> pdb=" O GLU M 65 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG M 70 " --> pdb=" O GLY M 66 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE M 76 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS M 77 " --> pdb=" O SER M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 93 removed outlier: 3.590A pdb=" N ARG M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 110 removed outlier: 3.851A pdb=" N LYS M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 14 removed outlier: 3.520A pdb=" N LYS N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 20 Processing helix chain 'N' and resid 23 through 32 removed outlier: 3.539A pdb=" N ILE N 29 " --> pdb=" O GLU N 25 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE N 30 " --> pdb=" O LEU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 46 removed outlier: 3.786A pdb=" N LYS N 46 " --> pdb=" O ASN N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 50 Processing helix chain 'N' and resid 55 through 59 removed outlier: 3.943A pdb=" N GLN N 59 " --> pdb=" O PRO N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 89 removed outlier: 4.538A pdb=" N GLU N 85 " --> pdb=" O ILE N 81 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET N 88 " --> pdb=" O ARG N 84 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 19 removed outlier: 5.431A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 74 removed outlier: 4.317A pdb=" N PHE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 127 through 128 removed outlier: 3.528A pdb=" N VAL D 124 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP D 140 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP D 173 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 14 Processing sheet with id=AA3, first strand: chain 'E' and resid 44 through 45 removed outlier: 3.736A pdb=" N VAL E 45 " --> pdb=" O ILE E 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 85 through 87 removed outlier: 6.652A pdb=" N ILE E 105 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA E 126 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 43 through 51 removed outlier: 3.507A pdb=" N ALA F 57 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 23 through 27 removed outlier: 4.174A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 75 through 76 removed outlier: 5.964A pdb=" N ILE H 124 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER H 104 " --> pdb=" O ILE H 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 42 through 45 removed outlier: 3.595A pdb=" N GLY K 42 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE K 30 " --> pdb=" O HIS K 23 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER K 16 " --> pdb=" O ILE K 78 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY K 18 " --> pdb=" O ASN K 80 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL K 83 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE K 109 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL K 85 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP K 111 " --> pdb=" O VAL K 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 29 through 30 Processing sheet with id=AB1, first strand: chain 'L' and resid 35 through 37 removed outlier: 3.793A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR L 94 " --> pdb=" O THR L 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 6 through 8 removed outlier: 4.184A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 6 through 8 removed outlier: 6.553A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 7 through 11 removed outlier: 7.761A pdb=" N GLN Q 8 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU Q 25 " --> pdb=" O GLN Q 8 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N LYS Q 70 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N HIS Q 44 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TRP Q 72 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU Q 74 " --> pdb=" O HIS Q 46 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER Q 71 " --> pdb=" O CYS Q 63 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL Q 77 " --> pdb=" O VAL Q 57 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL Q 57 " --> pdb=" O VAL Q 77 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE Q 60 " --> pdb=" O LEU Q 7 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 16 through 17 removed outlier: 3.628A pdb=" N HIS B 17 " --> pdb=" O HIS B 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB7, first strand: chain 'C' and resid 19 through 21 removed outlier: 3.974A pdb=" N ARG C 58 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE C 67 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 150 through 152 removed outlier: 3.725A pdb=" N VAL C 199 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 184 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 72 through 73 removed outlier: 3.832A pdb=" N GLU G 73 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL G 88 " --> pdb=" O GLU G 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 5 through 7 removed outlier: 4.054A pdb=" N PHE I 19 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL I 28 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL I 66 " --> pdb=" O VAL I 28 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 45 through 51 removed outlier: 3.715A pdb=" N GLU J 66 " --> pdb=" O LYS N 96 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 30 through 32 removed outlier: 5.179A pdb=" N LEU S 30 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N HIS S 51 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N THR S 32 " --> pdb=" O HIS S 51 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1249 hydrogen bonds 1900 hydrogen bond angles 0 basepair planarities 503 basepair parallelities 795 stacking parallelities Total time for adding SS restraints: 52.29 Time building geometry restraints manager: 35.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4558 1.29 - 1.42: 23997 1.42 - 1.56: 23559 1.56 - 1.69: 3059 1.69 - 1.82: 113 Bond restraints: 55286 Sorted by residual: bond pdb=" C6 A A 918 " pdb=" N1 A A 918 " ideal model delta sigma weight residual 1.351 1.248 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C2 U A 17 " pdb=" N3 U A 17 " ideal model delta sigma weight residual 1.373 1.296 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C4 U A 17 " pdb=" O4 U A 17 " ideal model delta sigma weight residual 1.232 1.161 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C5 G A1401 " pdb=" C6 G A1401 " ideal model delta sigma weight residual 1.419 1.350 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C2 C A1501 " pdb=" N3 C A1501 " ideal model delta sigma weight residual 1.353 1.290 0.063 2.00e-02 2.50e+03 1.00e+01 ... (remaining 55281 not shown) Histogram of bond angle deviations from ideal: 91.27 - 100.71: 227 100.71 - 110.16: 25884 110.16 - 119.60: 31501 119.60 - 129.04: 22915 129.04 - 138.48: 1688 Bond angle restraints: 82215 Sorted by residual: angle pdb=" OP1 A A 860 " pdb=" P A A 860 " pdb=" O5' A A 860 " ideal model delta sigma weight residual 108.00 91.27 16.73 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O4' G A1392 " pdb=" C1' G A1392 " pdb=" N9 G A1392 " ideal model delta sigma weight residual 108.20 116.37 -8.17 1.50e+00 4.44e-01 2.97e+01 angle pdb=" O3' G A 859 " pdb=" P A A 860 " pdb=" OP1 A A 860 " ideal model delta sigma weight residual 108.00 121.59 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" CA MET E 70 " pdb=" CB MET E 70 " pdb=" CG MET E 70 " ideal model delta sigma weight residual 114.10 105.22 8.88 2.00e+00 2.50e-01 1.97e+01 angle pdb=" O4' G A1505 " pdb=" C1' G A1505 " pdb=" N9 G A1505 " ideal model delta sigma weight residual 108.50 101.92 6.58 1.50e+00 4.44e-01 1.93e+01 ... (remaining 82210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 30956 35.90 - 71.79: 4002 71.79 - 107.69: 433 107.69 - 143.59: 11 143.59 - 179.48: 13 Dihedral angle restraints: 35415 sinusoidal: 28767 harmonic: 6648 Sorted by residual: dihedral pdb=" O4' U A1391 " pdb=" C1' U A1391 " pdb=" N1 U A1391 " pdb=" C2 U A1391 " ideal model delta sinusoidal sigma weight residual -160.00 10.58 -170.58 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U A 610 " pdb=" C1' U A 610 " pdb=" N1 U A 610 " pdb=" C2 U A 610 " ideal model delta sinusoidal sigma weight residual -160.00 2.87 -162.87 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sinusoidal sigma weight residual 200.00 53.67 146.33 1 1.50e+01 4.44e-03 7.82e+01 ... (remaining 35412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 9863 0.101 - 0.203: 534 0.203 - 0.304: 30 0.304 - 0.406: 4 0.406 - 0.507: 1 Chirality restraints: 10432 Sorted by residual: chirality pdb=" C1' G A1392 " pdb=" O4' G A1392 " pdb=" C2' G A1392 " pdb=" N9 G A1392 " both_signs ideal model delta sigma weight residual False 2.44 1.93 0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" C1' G A1530 " pdb=" O4' G A1530 " pdb=" C2' G A1530 " pdb=" N9 G A1530 " both_signs ideal model delta sigma weight residual False 2.46 2.12 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C3' A A 60 " pdb=" C4' A A 60 " pdb=" O3' A A 60 " pdb=" C2' A A 60 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 10429 not shown) Planarity restraints: 4743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 46 " -0.024 2.00e-02 2.50e+03 4.86e-02 2.37e+01 pdb=" C GLY E 46 " 0.084 2.00e-02 2.50e+03 pdb=" O GLY E 46 " -0.031 2.00e-02 2.50e+03 pdb=" N PHE E 47 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 199 " -0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO B 200 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 47 " 0.038 2.00e-02 2.50e+03 2.91e-02 1.48e+01 pdb=" CG PHE E 47 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE E 47 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 47 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 47 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 47 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE E 47 " 0.012 2.00e-02 2.50e+03 ... (remaining 4740 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 811 2.54 - 3.13: 42230 3.13 - 3.72: 106671 3.72 - 4.31: 145998 4.31 - 4.90: 195708 Nonbonded interactions: 491418 Sorted by model distance: nonbonded pdb=" O2 U A 157 " pdb=" O6 G A 164 " model vdw 1.947 2.432 nonbonded pdb=" N2 G A1421 " pdb=" O2 C A1479 " model vdw 2.024 2.496 nonbonded pdb=" O2 C A 940 " pdb=" N2 G A1343 " model vdw 2.029 2.496 nonbonded pdb=" O2 C A1096 " pdb=" O2' A A1170 " model vdw 2.033 2.440 nonbonded pdb=" O2 U A1351 " pdb=" N2 G A1371 " model vdw 2.038 2.496 ... (remaining 491413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 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: 0.050 Extract box with map and model: 16.110 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 183.670 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 209.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 55286 Z= 0.514 Angle : 0.929 16.727 82215 Z= 0.475 Chirality : 0.050 0.507 10432 Planarity : 0.006 0.115 4743 Dihedral : 23.982 179.482 31117 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 32.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.06 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.16), residues: 2278 helix: -2.13 (0.17), residues: 735 sheet: -2.96 (0.28), residues: 301 loop : -2.62 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP S 33 HIS 0.013 0.003 HIS C 5 PHE 0.065 0.004 PHE E 47 TYR 0.032 0.003 TYR L 37 ARG 0.017 0.001 ARG T 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 3.153 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: F 38 ARG cc_start: 0.6346 (ptp90) cc_final: 0.5758 (ptp90) REVERT: F 63 ASN cc_start: 0.6387 (t0) cc_final: 0.6151 (t0) REVERT: G 30 MET cc_start: 0.1064 (mtt) cc_final: 0.0546 (mtt) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.6707 time to fit residues: 401.1280 Evaluate side-chains 302 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 191 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 293 optimal weight: 20.0000 chunk 113 optimal weight: 40.0000 chunk 178 optimal weight: 0.0670 chunk 218 optimal weight: 5.9990 chunk 340 optimal weight: 8.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 HIS ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN I 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 55286 Z= 0.370 Angle : 0.787 11.647 82215 Z= 0.396 Chirality : 0.044 0.407 10432 Planarity : 0.006 0.089 4743 Dihedral : 24.850 176.928 26504 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 1.98 % Allowed : 10.07 % Favored : 87.95 % 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: -3.38 (0.16), residues: 2278 helix: -1.65 (0.17), residues: 765 sheet: -2.84 (0.27), residues: 303 loop : -2.50 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 21 HIS 0.011 0.002 HIS B 167 PHE 0.038 0.003 PHE E 47 TYR 0.042 0.002 TYR B 212 ARG 0.007 0.001 ARG U 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 346 time to evaluate : 3.014 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: E 63 MET cc_start: 0.4085 (mmm) cc_final: 0.3627 (mmm) REVERT: F 38 ARG cc_start: 0.6213 (ptp90) cc_final: 0.6006 (ptp90) REVERT: T 58 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6806 (m-30) REVERT: G 30 MET cc_start: 0.1062 (mtt) cc_final: 0.0321 (mtt) REVERT: M 68 LEU cc_start: 0.6107 (tt) cc_final: 0.4927 (mp) REVERT: M 69 ARG cc_start: 0.6093 (mmt180) cc_final: 0.5476 (mmp-170) REVERT: S 5 LYS cc_start: 0.5051 (mptt) cc_final: 0.4578 (mptt) outliers start: 38 outliers final: 23 residues processed: 362 average time/residue: 0.6853 time to fit residues: 406.3450 Evaluate side-chains 326 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 302 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 39 ASN Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain R residue 73 HIS Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain T residue 60 GLN Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain S residue 70 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 8.9990 chunk 105 optimal weight: 30.0000 chunk 283 optimal weight: 0.0770 chunk 231 optimal weight: 10.0000 chunk 93 optimal weight: 30.0000 chunk 341 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 chunk 303 optimal weight: 4.9990 chunk 338 optimal weight: 30.0000 chunk 116 optimal weight: 9.9990 chunk 273 optimal weight: 7.9990 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 HIS ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 ASN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN C 101 ASN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** N 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 55286 Z= 0.414 Angle : 0.808 14.040 82215 Z= 0.403 Chirality : 0.045 0.418 10432 Planarity : 0.006 0.071 4743 Dihedral : 24.755 174.190 26504 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 26.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.48 % Favored : 86.52 % Rotamer: Outliers : 3.13 % Allowed : 15.49 % Favored : 81.38 % 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: -3.38 (0.16), residues: 2278 helix: -1.61 (0.17), residues: 775 sheet: -2.86 (0.27), residues: 312 loop : -2.52 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 21 HIS 0.008 0.002 HIS L 95 PHE 0.035 0.003 PHE E 47 TYR 0.036 0.002 TYR B 212 ARG 0.009 0.001 ARG U 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 319 time to evaluate : 3.183 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: D 104 MET cc_start: 0.7622 (mmm) cc_final: 0.7400 (mmm) REVERT: E 71 ILE cc_start: 0.4832 (OUTLIER) cc_final: 0.4233 (pt) REVERT: F 38 ARG cc_start: 0.6212 (ptp90) cc_final: 0.5948 (ptp90) REVERT: F 63 ASN cc_start: 0.6769 (t0) cc_final: 0.6552 (t0) REVERT: T 58 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6897 (m-30) REVERT: G 30 MET cc_start: 0.1138 (mtt) cc_final: 0.0296 (mtt) REVERT: I 36 GLN cc_start: 0.6929 (mp10) cc_final: 0.6605 (pt0) REVERT: S 5 LYS cc_start: 0.4913 (mptt) cc_final: 0.4112 (mptt) outliers start: 60 outliers final: 33 residues processed: 352 average time/residue: 0.7015 time to fit residues: 397.8019 Evaluate side-chains 313 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 278 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 39 ASN Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain R residue 73 HIS Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 70 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 342 optimal weight: 30.0000 chunk 362 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 324 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** N 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 55286 Z= 0.283 Angle : 0.695 10.299 82215 Z= 0.350 Chirality : 0.040 0.418 10432 Planarity : 0.005 0.057 4743 Dihedral : 24.570 175.898 26504 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 3.08 % Allowed : 18.00 % Favored : 78.93 % 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: -3.06 (0.17), residues: 2278 helix: -1.33 (0.18), residues: 789 sheet: -2.67 (0.28), residues: 311 loop : -2.35 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 103 HIS 0.006 0.001 HIS F 3 PHE 0.023 0.002 PHE E 47 TYR 0.039 0.002 TYR B 212 ARG 0.006 0.001 ARG R 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 317 time to evaluate : 3.370 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: E 71 ILE cc_start: 0.4520 (OUTLIER) cc_final: 0.2642 (tp) REVERT: F 38 ARG cc_start: 0.6269 (ptp90) cc_final: 0.6062 (ptp90) REVERT: L 61 GLU cc_start: 0.6008 (mp0) cc_final: 0.5788 (mp0) REVERT: O 1 SER cc_start: 0.6760 (p) cc_final: 0.6548 (t) REVERT: T 58 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6741 (m-30) REVERT: U 38 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5518 (pp20) REVERT: G 30 MET cc_start: 0.1212 (mtt) cc_final: 0.0533 (mtt) REVERT: G 100 MET cc_start: 0.5351 (tpt) cc_final: 0.5045 (tpt) REVERT: S 5 LYS cc_start: 0.4878 (mptt) cc_final: 0.4074 (mptt) outliers start: 59 outliers final: 31 residues processed: 362 average time/residue: 0.7004 time to fit residues: 413.1157 Evaluate side-chains 327 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 293 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain R residue 73 HIS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain T residue 60 GLN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain S residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 269 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 309 optimal weight: 30.0000 chunk 250 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 325 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 55286 Z= 0.306 Angle : 0.712 13.887 82215 Z= 0.358 Chirality : 0.040 0.423 10432 Planarity : 0.005 0.047 4743 Dihedral : 24.551 176.431 26504 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 3.23 % Allowed : 19.93 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.17), residues: 2278 helix: -1.14 (0.18), residues: 767 sheet: -2.65 (0.27), residues: 316 loop : -2.32 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 103 HIS 0.007 0.001 HIS N 70 PHE 0.023 0.002 PHE E 47 TYR 0.040 0.002 TYR B 212 ARG 0.007 0.001 ARG H 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 311 time to evaluate : 3.121 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: E 71 ILE cc_start: 0.4666 (OUTLIER) cc_final: 0.2803 (tp) REVERT: H 65 PHE cc_start: 0.6392 (t80) cc_final: 0.6152 (t80) REVERT: O 1 SER cc_start: 0.6883 (p) cc_final: 0.6610 (t) REVERT: T 58 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: G 30 MET cc_start: 0.1175 (mtt) cc_final: 0.0416 (mtt) REVERT: G 100 MET cc_start: 0.5483 (tpt) cc_final: 0.5143 (tpt) REVERT: S 5 LYS cc_start: 0.4938 (mptt) cc_final: 0.4070 (mptt) outliers start: 62 outliers final: 46 residues processed: 353 average time/residue: 0.7299 time to fit residues: 419.5423 Evaluate side-chains 340 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 292 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain T residue 60 GLN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain S residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 40.0000 chunk 326 optimal weight: 0.0570 chunk 71 optimal weight: 7.9990 chunk 212 optimal weight: 30.0000 chunk 89 optimal weight: 7.9990 chunk 362 optimal weight: 0.3980 chunk 301 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 120 optimal weight: 30.0000 chunk 190 optimal weight: 5.9990 overall best weight: 3.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS H 75 GLN K 14 GLN L 71 HIS ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 55286 Z= 0.302 Angle : 0.707 9.649 82215 Z= 0.356 Chirality : 0.040 0.427 10432 Planarity : 0.005 0.045 4743 Dihedral : 24.510 176.995 26504 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 4.17 % Allowed : 20.40 % Favored : 75.43 % 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: -2.85 (0.17), residues: 2278 helix: -1.07 (0.18), residues: 767 sheet: -2.56 (0.27), residues: 320 loop : -2.26 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.013 0.001 HIS B 17 PHE 0.030 0.002 PHE H 65 TYR 0.037 0.002 TYR B 212 ARG 0.007 0.001 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 317 time to evaluate : 4.088 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: E 71 ILE cc_start: 0.4587 (OUTLIER) cc_final: 0.2664 (tp) REVERT: F 38 ARG cc_start: 0.5726 (ptp90) cc_final: 0.5414 (ptp90) REVERT: L 37 TYR cc_start: 0.6262 (m-80) cc_final: 0.5991 (m-10) REVERT: O 1 SER cc_start: 0.6876 (OUTLIER) cc_final: 0.6619 (t) REVERT: T 58 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6832 (m-30) REVERT: U 38 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5569 (pp20) REVERT: C 143 LEU cc_start: 0.6613 (mm) cc_final: 0.6412 (mm) REVERT: G 30 MET cc_start: 0.1216 (mtt) cc_final: 0.0371 (mtt) REVERT: G 100 MET cc_start: 0.5433 (tpt) cc_final: 0.5200 (tpt) REVERT: M 56 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6631 (ptp-170) REVERT: S 5 LYS cc_start: 0.4925 (mptt) cc_final: 0.3991 (mptt) outliers start: 80 outliers final: 52 residues processed: 375 average time/residue: 0.6918 time to fit residues: 417.2478 Evaluate side-chains 348 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 291 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 73 HIS Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain T residue 60 GLN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain S residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 264 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 361 optimal weight: 20.0000 chunk 226 optimal weight: 0.9990 chunk 220 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS H 66 GLN H 75 GLN K 21 HIS K 80 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 55286 Z= 0.186 Angle : 0.628 11.362 82215 Z= 0.317 Chirality : 0.036 0.424 10432 Planarity : 0.004 0.051 4743 Dihedral : 24.349 177.000 26504 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 3.23 % Allowed : 22.74 % Favored : 74.02 % 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: -2.61 (0.17), residues: 2278 helix: -0.83 (0.19), residues: 772 sheet: -2.34 (0.28), residues: 307 loop : -2.19 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 103 HIS 0.007 0.001 HIS B 17 PHE 0.033 0.002 PHE H 65 TYR 0.039 0.002 TYR B 212 ARG 0.006 0.001 ARG T 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 327 time to evaluate : 3.427 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: E 71 ILE cc_start: 0.4192 (OUTLIER) cc_final: 0.2329 (tp) REVERT: E 144 GLU cc_start: 0.6170 (mm-30) cc_final: 0.5837 (mm-30) REVERT: L 13 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6193 (tpm170) REVERT: T 58 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6743 (m-30) REVERT: U 38 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5401 (pp20) REVERT: U 46 ARG cc_start: 0.4176 (tpt90) cc_final: 0.3391 (mtp180) REVERT: G 30 MET cc_start: 0.1283 (mtt) cc_final: 0.0379 (mtt) REVERT: M 69 ARG cc_start: 0.6290 (mmt180) cc_final: 0.5426 (mmt180) REVERT: S 5 LYS cc_start: 0.4867 (mptt) cc_final: 0.4194 (mptt) REVERT: S 54 ARG cc_start: 0.6322 (mmp80) cc_final: 0.5823 (mmt180) outliers start: 62 outliers final: 44 residues processed: 367 average time/residue: 0.6940 time to fit residues: 410.7155 Evaluate side-chains 346 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 298 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 73 HIS Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain T residue 60 GLN Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 0.2980 chunk 144 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS K 80 ASN T 77 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 55286 Z= 0.197 Angle : 0.633 11.184 82215 Z= 0.320 Chirality : 0.036 0.427 10432 Planarity : 0.004 0.042 4743 Dihedral : 24.290 177.177 26504 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 3.55 % Allowed : 23.21 % Favored : 73.24 % 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: -2.50 (0.17), residues: 2278 helix: -0.75 (0.19), residues: 773 sheet: -2.25 (0.29), residues: 303 loop : -2.13 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.006 0.001 HIS L 76 PHE 0.032 0.002 PHE H 65 TYR 0.039 0.002 TYR B 212 ARG 0.011 0.001 ARG I 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 314 time to evaluate : 3.168 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: D 163 GLN cc_start: 0.6906 (pm20) cc_final: 0.6253 (pm20) REVERT: E 71 ILE cc_start: 0.4489 (OUTLIER) cc_final: 0.2563 (tp) REVERT: F 75 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7453 (mm-30) REVERT: K 55 ARG cc_start: 0.5526 (mpp-170) cc_final: 0.3189 (mtt180) REVERT: L 13 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6253 (tpm170) REVERT: T 58 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6702 (m-30) REVERT: T 77 ASN cc_start: 0.8182 (m-40) cc_final: 0.7940 (m-40) REVERT: U 38 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5320 (pp20) REVERT: M 69 ARG cc_start: 0.6340 (mmt180) cc_final: 0.5290 (mmt180) REVERT: N 88 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5779 (tmm) REVERT: S 5 LYS cc_start: 0.4751 (mptt) cc_final: 0.4017 (mptt) REVERT: S 43 MET cc_start: 0.1859 (mmt) cc_final: 0.1335 (mmt) outliers start: 68 outliers final: 56 residues processed: 355 average time/residue: 0.6897 time to fit residues: 396.3599 Evaluate side-chains 357 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 296 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 73 HIS Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain T residue 60 GLN Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain S residue 55 GLN Chi-restraints excluded: chain S residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 20.0000 chunk 346 optimal weight: 50.0000 chunk 315 optimal weight: 50.0000 chunk 336 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 146 optimal weight: 20.0000 chunk 264 optimal weight: 0.8980 chunk 103 optimal weight: 30.0000 chunk 304 optimal weight: 9.9990 chunk 318 optimal weight: 3.9990 chunk 335 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS F 94 HIS ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 55286 Z= 0.281 Angle : 0.692 11.146 82215 Z= 0.348 Chirality : 0.038 0.431 10432 Planarity : 0.005 0.053 4743 Dihedral : 24.335 176.772 26504 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 4.02 % Allowed : 23.63 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.17), residues: 2278 helix: -0.77 (0.19), residues: 770 sheet: -2.27 (0.29), residues: 303 loop : -2.17 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 103 HIS 0.027 0.002 HIS B 17 PHE 0.030 0.002 PHE F 8 TYR 0.039 0.002 TYR B 212 ARG 0.009 0.001 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 297 time to evaluate : 3.059 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: D 163 GLN cc_start: 0.6877 (pm20) cc_final: 0.6299 (pm20) REVERT: K 35 ASP cc_start: 0.6752 (p0) cc_final: 0.6404 (p0) REVERT: K 55 ARG cc_start: 0.5734 (mpp-170) cc_final: 0.3465 (mtt180) REVERT: L 13 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6282 (tpm170) REVERT: O 25 GLU cc_start: 0.7193 (pm20) cc_final: 0.6964 (pm20) REVERT: T 58 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6790 (m-30) REVERT: T 77 ASN cc_start: 0.8266 (m-40) cc_final: 0.8061 (m-40) REVERT: U 38 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5344 (pp20) REVERT: M 69 ARG cc_start: 0.6463 (mmt180) cc_final: 0.5383 (mmt180) REVERT: N 88 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.5803 (tmm) REVERT: S 5 LYS cc_start: 0.4746 (mptt) cc_final: 0.3977 (mptt) outliers start: 77 outliers final: 55 residues processed: 348 average time/residue: 0.6846 time to fit residues: 382.5092 Evaluate side-chains 347 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 288 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain T residue 60 GLN Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain S residue 55 GLN Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain S residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 1.9990 chunk 356 optimal weight: 30.0000 chunk 217 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 247 optimal weight: 0.9990 chunk 373 optimal weight: 9.9990 chunk 343 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 229 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 GLN ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 55286 Z= 0.259 Angle : 0.675 11.473 82215 Z= 0.340 Chirality : 0.038 0.431 10432 Planarity : 0.005 0.039 4743 Dihedral : 24.321 176.199 26504 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 3.29 % Allowed : 24.62 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.17), residues: 2278 helix: -0.75 (0.19), residues: 768 sheet: -2.15 (0.29), residues: 308 loop : -2.11 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.025 0.002 HIS B 17 PHE 0.040 0.002 PHE F 8 TYR 0.041 0.002 TYR B 212 ARG 0.008 0.001 ARG L 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 297 time to evaluate : 3.177 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: D 163 GLN cc_start: 0.6952 (pm20) cc_final: 0.6385 (pm20) REVERT: K 35 ASP cc_start: 0.6792 (p0) cc_final: 0.6433 (p0) REVERT: K 55 ARG cc_start: 0.5765 (mpp-170) cc_final: 0.3665 (mtt180) REVERT: L 13 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6328 (tpm170) REVERT: O 25 GLU cc_start: 0.7130 (pm20) cc_final: 0.6907 (pm20) REVERT: T 58 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6818 (m-30) REVERT: T 77 ASN cc_start: 0.8252 (m-40) cc_final: 0.8049 (m-40) REVERT: B 153 MET cc_start: 0.6914 (ppp) cc_final: 0.6661 (ppp) REVERT: B 183 PHE cc_start: 0.7449 (m-10) cc_final: 0.7148 (m-10) REVERT: U 38 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5414 (pp20) REVERT: G 30 MET cc_start: -0.0063 (mtt) cc_final: -0.0938 (mtt) REVERT: M 69 ARG cc_start: 0.6523 (mmt180) cc_final: 0.5465 (mmt180) REVERT: S 5 LYS cc_start: 0.4619 (mptt) cc_final: 0.3876 (mptt) outliers start: 63 outliers final: 51 residues processed: 339 average time/residue: 0.6967 time to fit residues: 381.4211 Evaluate side-chains 342 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 288 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain T residue 60 GLN Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain S residue 55 GLN Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain S residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 0.8980 chunk 316 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 124 optimal weight: 30.0000 chunk 305 optimal weight: 0.0770 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS F 94 HIS K 80 ASN L 76 HIS ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.140909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.114974 restraints weight = 152078.784| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.85 r_work: 0.3638 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 55286 Z= 0.228 Angle : 0.657 11.271 82215 Z= 0.331 Chirality : 0.036 0.431 10432 Planarity : 0.005 0.043 4743 Dihedral : 24.282 175.695 26504 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 3.50 % Allowed : 24.78 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.17), residues: 2278 helix: -0.72 (0.19), residues: 767 sheet: -2.12 (0.29), residues: 309 loop : -2.09 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 103 HIS 0.022 0.002 HIS B 17 PHE 0.034 0.002 PHE F 8 TYR 0.040 0.002 TYR B 212 ARG 0.007 0.001 ARG L 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10963.51 seconds wall clock time: 201 minutes 15.22 seconds (12075.22 seconds total)