Starting phenix.real_space_refine on Fri Mar 15 18:25:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/03_2024/7cgp_9958_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/03_2024/7cgp_9958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/03_2024/7cgp_9958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/03_2024/7cgp_9958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/03_2024/7cgp_9958_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/03_2024/7cgp_9958_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 1 5.49 5 S 122 5.16 5 C 7823 2.51 5 N 2158 2.21 5 O 2329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "F GLU 50": "OE1" <-> "OE2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I GLU 40": "OE1" <-> "OE2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "J ARG 23": "NH1" <-> "NH2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K ARG 39": "NH1" <-> "NH2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "M GLU 12": "OE1" <-> "OE2" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M ARG 24": "NH1" <-> "NH2" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N GLU 40": "OE1" <-> "OE2" Residue "N GLU 71": "OE1" <-> "OE2" Residue "O ARG 5": "NH1" <-> "NH2" Residue "O ARG 24": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12433 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1068 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain breaks: 1 Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2696 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 326} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1684 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'TRP:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 554 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 558 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 521 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 61} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 569 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 502 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 61} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "J" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 680 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "K" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 590 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 646 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "M" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 589 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 580 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "O" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.86, per 1000 atoms: 0.55 Number of scatterers: 12433 At special positions: 0 Unit cell: (121.68, 113.568, 172.38, 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 122 16.00 P 1 15.00 O 2329 8.00 N 2158 7.00 C 7823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 141 " distance=2.02 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 52 " distance=2.04 Simple disulfide: pdb=" SG CYS D 32 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 52 " distance=2.03 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 48 " distance=2.03 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 52 " distance=2.03 Simple disulfide: pdb=" SG CYS F 32 " - pdb=" SG CYS F 48 " distance=2.03 Simple disulfide: pdb=" SG CYS G 29 " - pdb=" SG CYS G 54 " distance=2.03 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 50 " distance=2.03 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 54 " distance=2.03 Simple disulfide: pdb=" SG CYS H 33 " - pdb=" SG CYS H 50 " distance=2.03 Simple disulfide: pdb=" SG CYS I 29 " - pdb=" SG CYS I 54 " distance=2.03 Simple disulfide: pdb=" SG CYS I 33 " - pdb=" SG CYS I 50 " distance=2.02 Simple disulfide: pdb=" SG CYS J 28 " - pdb=" SG CYS J 52 " distance=2.03 Simple disulfide: pdb=" SG CYS J 32 " - pdb=" SG CYS J 48 " distance=2.03 Simple disulfide: pdb=" SG CYS K 28 " - pdb=" SG CYS K 52 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 48 " distance=2.03 Simple disulfide: pdb=" SG CYS L 28 " - pdb=" SG CYS L 52 " distance=2.04 Simple disulfide: pdb=" SG CYS L 32 " - pdb=" SG CYS L 48 " distance=2.03 Simple disulfide: pdb=" SG CYS M 29 " - pdb=" SG CYS M 54 " distance=2.04 Simple disulfide: pdb=" SG CYS M 33 " - pdb=" SG CYS M 50 " distance=2.03 Simple disulfide: pdb=" SG CYS N 29 " - pdb=" SG CYS N 54 " distance=2.03 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 50 " distance=2.02 Simple disulfide: pdb=" SG CYS O 29 " - pdb=" SG CYS O 54 " distance=2.04 Simple disulfide: pdb=" SG CYS O 33 " - pdb=" SG CYS O 50 " distance=2.03 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: 5.05 Conformation dependent library (CDL) restraints added in 2.1 seconds 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 4 sheets defined 66.5% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 removed outlier: 4.342A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 92 Processing helix chain 'A' and resid 121 through 147 Processing helix chain 'A' and resid 152 through 170 Processing helix chain 'A' and resid 172 through 192 removed outlier: 3.572A pdb=" N ALA A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 50 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 103 through 111 Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.609A pdb=" N LEU B 164 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 184 removed outlier: 3.956A pdb=" N ILE B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.940A pdb=" N ILE B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N HIS B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.720A pdb=" N ARG B 351 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'C' and resid 22 through 54 Processing helix chain 'C' and resid 58 through 74 Processing helix chain 'C' and resid 79 through 96 removed outlier: 4.557A pdb=" N GLU C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 Processing helix chain 'C' and resid 145 through 148 No H-bonds generated for 'chain 'C' and resid 145 through 148' Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 175 through 178 No H-bonds generated for 'chain 'C' and resid 175 through 178' Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.092A pdb=" N LYS C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 243 Processing helix chain 'D' and resid 14 through 31 Processing helix chain 'D' and resid 43 through 76 removed outlier: 3.631A pdb=" N LEU D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 29 removed outlier: 4.037A pdb=" N GLU E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 74 Processing helix chain 'F' and resid 15 through 32 Processing helix chain 'F' and resid 43 through 74 removed outlier: 4.130A pdb=" N GLN F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 32 removed outlier: 3.621A pdb=" N MET G 21 " --> pdb=" O MET G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.114A pdb=" N ASP G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU G 72 " --> pdb=" O LYS G 68 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET G 74 " --> pdb=" O THR G 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 33 Processing helix chain 'H' and resid 45 through 74 removed outlier: 4.004A pdb=" N ASP H 52 " --> pdb=" O SER H 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 33 removed outlier: 3.746A pdb=" N SER I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS I 32 " --> pdb=" O ALA I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 48 No H-bonds generated for 'chain 'I' and resid 45 through 48' Processing helix chain 'I' and resid 50 through 72 removed outlier: 4.013A pdb=" N SER I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU I 72 " --> pdb=" O LYS I 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 30 Processing helix chain 'J' and resid 43 through 84 Proline residue: J 72 - end of helix Processing helix chain 'K' and resid 9 through 32 Processing helix chain 'K' and resid 46 through 76 removed outlier: 3.998A pdb=" N GLU K 50 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 32 removed outlier: 3.784A pdb=" N GLN L 10 " --> pdb=" O PRO L 6 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN L 13 " --> pdb=" O ASP L 9 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR L 27 " --> pdb=" O LYS L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 81 removed outlier: 4.397A pdb=" N SER L 49 " --> pdb=" O GLU L 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 33 Processing helix chain 'M' and resid 46 through 74 removed outlier: 4.673A pdb=" N LEU M 51 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE M 61 " --> pdb=" O LYS M 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 33 removed outlier: 3.593A pdb=" N CYS N 33 " --> pdb=" O CYS N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 58 removed outlier: 3.881A pdb=" N ASP N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 72 removed outlier: 3.752A pdb=" N GLY N 66 " --> pdb=" O HIS N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 33 removed outlier: 3.970A pdb=" N SER O 27 " --> pdb=" O ASN O 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG O 31 " --> pdb=" O SER O 27 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 76 removed outlier: 4.116A pdb=" N ASP O 52 " --> pdb=" O SER O 48 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS O 57 " --> pdb=" O ARG O 53 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU O 59 " --> pdb=" O VAL O 55 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP O 60 " --> pdb=" O SER O 56 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 94 through 99 removed outlier: 7.041A pdb=" N VAL B 118 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N PHE B 66 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 120 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N VAL B 121 " --> pdb=" O PRO B 148 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY B 150 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 188 through 190 Processing sheet with id= C, first strand: chain 'B' and resid 202 through 205 Processing sheet with id= D, first strand: chain 'B' and resid 208 through 212 804 hydrogen bonds defined for protein. 2391 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2477 1.33 - 1.45: 2878 1.45 - 1.58: 7115 1.58 - 1.70: 2 1.70 - 1.82: 179 Bond restraints: 12651 Sorted by residual: bond pdb=" N VAL C 22 " pdb=" CA VAL C 22 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.98e+00 bond pdb=" N VAL C 27 " pdb=" CA VAL C 27 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.70e+00 bond pdb=" N LEU B 227 " pdb=" CA LEU B 227 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.19e-02 7.06e+03 7.53e+00 bond pdb=" N LYS C 24 " pdb=" CA LYS C 24 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.04e-02 9.25e+03 7.43e+00 bond pdb=" N THR B 157 " pdb=" CA THR B 157 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.08e+00 ... (remaining 12646 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.91: 247 105.91 - 113.00: 6851 113.00 - 120.09: 4600 120.09 - 127.18: 5196 127.18 - 134.27: 114 Bond angle restraints: 17008 Sorted by residual: angle pdb=" N VAL M 49 " pdb=" CA VAL M 49 " pdb=" C VAL M 49 " ideal model delta sigma weight residual 112.96 108.20 4.76 1.00e+00 1.00e+00 2.27e+01 angle pdb=" N LEU B 154 " pdb=" CA LEU B 154 " pdb=" C LEU B 154 " ideal model delta sigma weight residual 112.89 108.17 4.72 1.24e+00 6.50e-01 1.45e+01 angle pdb=" C ASP F 31 " pdb=" N CYS F 32 " pdb=" CA CYS F 32 " ideal model delta sigma weight residual 122.56 117.21 5.35 1.50e+00 4.44e-01 1.27e+01 angle pdb=" N ARG C 197 " pdb=" CA ARG C 197 " pdb=" C ARG C 197 " ideal model delta sigma weight residual 113.50 109.23 4.27 1.23e+00 6.61e-01 1.21e+01 angle pdb=" O3P PEE C 301 " pdb=" P PEE C 301 " pdb=" O4P PEE C 301 " ideal model delta sigma weight residual 92.91 103.08 -10.17 3.00e+00 1.11e-01 1.15e+01 ... (remaining 17003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.79: 7562 30.79 - 61.58: 262 61.58 - 92.37: 25 92.37 - 123.16: 2 123.16 - 153.96: 3 Dihedral angle restraints: 7854 sinusoidal: 3274 harmonic: 4580 Sorted by residual: dihedral pdb=" CB CYS F 32 " pdb=" SG CYS F 32 " pdb=" SG CYS F 48 " pdb=" CB CYS F 48 " ideal model delta sinusoidal sigma weight residual 93.00 52.07 40.93 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" C4 PEE C 301 " pdb=" O4P PEE C 301 " pdb=" P PEE C 301 " pdb=" O1P PEE C 301 " ideal model delta sinusoidal sigma weight residual 57.28 -148.76 -153.96 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C3 PEE C 301 " pdb=" C1 PEE C 301 " pdb=" C2 PEE C 301 " pdb=" O3P PEE C 301 " ideal model delta sinusoidal sigma weight residual 62.73 -82.54 145.27 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 7851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1558 0.051 - 0.102: 262 0.102 - 0.153: 43 0.153 - 0.204: 9 0.204 - 0.254: 1 Chirality restraints: 1873 Sorted by residual: chirality pdb=" CA VAL C 198 " pdb=" N VAL C 198 " pdb=" C VAL C 198 " pdb=" CB VAL C 198 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LEU B 154 " pdb=" N LEU B 154 " pdb=" C LEU B 154 " pdb=" CB LEU B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA VAL C 27 " pdb=" N VAL C 27 " pdb=" C VAL C 27 " pdb=" CB VAL C 27 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 1870 not shown) Planarity restraints: 2183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 196 " 0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C LEU C 196 " -0.071 2.00e-02 2.50e+03 pdb=" O LEU C 196 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG C 197 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 34 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO G 35 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO G 35 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 35 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 47 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C GLU N 47 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU N 47 " -0.010 2.00e-02 2.50e+03 pdb=" N SER N 48 " -0.009 2.00e-02 2.50e+03 ... (remaining 2180 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 79 2.46 - 3.07: 9319 3.07 - 3.68: 18777 3.68 - 4.29: 25805 4.29 - 4.90: 42724 Nonbonded interactions: 96704 Sorted by model distance: nonbonded pdb=" OH TYR D 70 " pdb=" OE2 GLU G 63 " model vdw 1.852 2.440 nonbonded pdb=" O ILE B 335 " pdb=" OG1 THR B 363 " model vdw 1.882 2.440 nonbonded pdb=" NE2 GLN K 74 " pdb=" OE2 GLU O 63 " model vdw 1.951 2.520 nonbonded pdb=" OE2 GLU A 144 " pdb=" OG SER A 150 " model vdw 2.036 2.440 nonbonded pdb=" OH TYR F 21 " pdb=" O HIS G 62 " model vdw 2.068 2.440 ... (remaining 96699 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 13 through 72 or (resid 73 through 75 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 13 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 73 or (resid 74 through 75 and (na \ me N or name CA or name C or name O or name CB )))) selection = chain 'F' selection = (chain 'K' and (resid 13 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 72 or (resid 73 through 75 and (na \ me N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'G' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 72 or (r \ esid 73 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 69 through 72 or (resid 73 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'I' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 73)) selection = (chain 'M' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 72 or (r \ esid 73 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'N' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 72 or (r \ esid 73 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'O' and (resid 10 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 69 through 72 or (resid 73 and ( \ name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.410 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 34.700 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.006 0.057 12651 Z= 0.400 Angle : 0.659 10.173 17008 Z= 0.424 Chirality : 0.041 0.254 1873 Planarity : 0.003 0.050 2183 Dihedral : 15.247 153.956 4800 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.53 % Allowed : 3.01 % Favored : 96.47 % 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: -2.68 (0.19), residues: 1531 helix: -0.96 (0.14), residues: 1038 sheet: -2.91 (0.44), residues: 105 loop : -3.36 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 28 HIS 0.012 0.001 HIS O 37 PHE 0.015 0.001 PHE B 80 TYR 0.023 0.002 TYR L 21 ARG 0.008 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 582 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7189 (ttp) cc_final: 0.6917 (mmt) REVERT: A 185 PHE cc_start: 0.8449 (t80) cc_final: 0.8159 (t80) REVERT: B 215 ARG cc_start: 0.7604 (tmt170) cc_final: 0.6615 (ttt-90) REVERT: B 219 VAL cc_start: 0.8842 (t) cc_final: 0.8623 (t) REVERT: B 329 ASP cc_start: 0.6102 (p0) cc_final: 0.5485 (p0) REVERT: C 76 LEU cc_start: 0.7117 (tp) cc_final: 0.6602 (pt) REVERT: C 206 SER cc_start: 0.9123 (p) cc_final: 0.8914 (p) REVERT: C 218 LYS cc_start: 0.8945 (mtmm) cc_final: 0.8277 (tmtt) REVERT: D 57 LEU cc_start: 0.8841 (mt) cc_final: 0.7463 (mt) REVERT: E 18 LEU cc_start: 0.8662 (mt) cc_final: 0.8353 (pp) REVERT: E 22 ASN cc_start: 0.8532 (p0) cc_final: 0.8114 (p0) REVERT: E 51 HIS cc_start: 0.8472 (m170) cc_final: 0.7961 (m170) REVERT: E 58 LYS cc_start: 0.9363 (mtpt) cc_final: 0.8627 (mmmt) REVERT: E 60 THR cc_start: 0.9588 (m) cc_final: 0.9364 (p) REVERT: F 23 LYS cc_start: 0.8724 (mtmm) cc_final: 0.8465 (mttp) REVERT: F 62 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7341 (ttm-80) REVERT: G 20 ASP cc_start: 0.8188 (t70) cc_final: 0.7908 (t0) REVERT: H 40 GLU cc_start: 0.8528 (mp0) cc_final: 0.8273 (mp0) REVERT: H 49 VAL cc_start: 0.9229 (t) cc_final: 0.9003 (p) REVERT: H 57 LYS cc_start: 0.9419 (mttt) cc_final: 0.9122 (mtpt) REVERT: I 17 MET cc_start: 0.8927 (tpt) cc_final: 0.8683 (tmm) REVERT: I 21 MET cc_start: 0.8971 (tmm) cc_final: 0.8089 (tmm) REVERT: I 25 MET cc_start: 0.8851 (ptp) cc_final: 0.7498 (ptm) REVERT: I 44 SER cc_start: 0.7704 (m) cc_final: 0.7374 (p) REVERT: I 58 TYR cc_start: 0.8705 (t80) cc_final: 0.7844 (t80) REVERT: I 65 MET cc_start: 0.8711 (tpp) cc_final: 0.8291 (tpp) REVERT: I 69 LEU cc_start: 0.8593 (mm) cc_final: 0.7971 (mm) REVERT: M 14 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7985 (tm-30) REVERT: M 52 ASP cc_start: 0.7813 (m-30) cc_final: 0.7596 (m-30) REVERT: M 64 ARG cc_start: 0.7566 (mtt-85) cc_final: 0.7143 (mtt-85) REVERT: O 42 GLU cc_start: 0.7814 (tp30) cc_final: 0.7286 (tp30) outliers start: 7 outliers final: 5 residues processed: 586 average time/residue: 0.2980 time to fit residues: 230.8202 Evaluate side-chains 426 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 421 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 198 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 HIS G 62 HIS ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 HIS L 71 HIS M 30 HIS N 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 12651 Z= 0.274 Angle : 0.723 13.223 17008 Z= 0.369 Chirality : 0.044 0.307 1873 Planarity : 0.004 0.045 2183 Dihedral : 10.264 156.137 1744 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.53 % Allowed : 17.52 % Favored : 78.95 % 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: -0.29 (0.21), residues: 1531 helix: 0.86 (0.16), residues: 1037 sheet: -2.32 (0.40), residues: 116 loop : -2.35 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 28 HIS 0.010 0.001 HIS I 62 PHE 0.022 0.002 PHE A 81 TYR 0.017 0.002 TYR M 22 ARG 0.007 0.001 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 480 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7320 (ttp) cc_final: 0.6985 (mmt) REVERT: A 140 GLU cc_start: 0.8368 (pp20) cc_final: 0.7413 (tp30) REVERT: A 185 PHE cc_start: 0.8420 (t80) cc_final: 0.8167 (t80) REVERT: B 241 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 329 ASP cc_start: 0.6267 (p0) cc_final: 0.5811 (p0) REVERT: C 76 LEU cc_start: 0.6703 (tp) cc_final: 0.6389 (pp) REVERT: C 134 TYR cc_start: 0.8907 (p90) cc_final: 0.8645 (p90) REVERT: C 143 SER cc_start: 0.9171 (t) cc_final: 0.8643 (t) REVERT: C 218 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8180 (tmtt) REVERT: E 18 LEU cc_start: 0.8658 (mt) cc_final: 0.8412 (pp) REVERT: E 51 HIS cc_start: 0.8358 (m170) cc_final: 0.7964 (m170) REVERT: E 58 LYS cc_start: 0.9217 (mtpt) cc_final: 0.8837 (mmmt) REVERT: E 66 ARG cc_start: 0.7997 (tpt170) cc_final: 0.7639 (tpt90) REVERT: E 69 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8423 (mt-10) REVERT: F 62 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.6560 (ttm-80) REVERT: F 66 ARG cc_start: 0.8974 (tpp-160) cc_final: 0.8194 (mpp-170) REVERT: G 13 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.7764 (tp) REVERT: G 20 ASP cc_start: 0.8354 (t70) cc_final: 0.8026 (t0) REVERT: G 31 ARG cc_start: 0.9048 (ttm-80) cc_final: 0.8516 (ttm-80) REVERT: I 14 GLU cc_start: 0.8753 (tp30) cc_final: 0.8439 (tp30) REVERT: I 21 MET cc_start: 0.9096 (tmm) cc_final: 0.8228 (tmm) REVERT: I 25 MET cc_start: 0.8702 (ptp) cc_final: 0.7528 (ptm) REVERT: I 58 TYR cc_start: 0.8697 (t80) cc_final: 0.7986 (t80) REVERT: I 60 ASP cc_start: 0.9002 (t0) cc_final: 0.8652 (t0) REVERT: I 63 GLU cc_start: 0.9038 (pt0) cc_final: 0.8755 (pp20) REVERT: I 64 ARG cc_start: 0.8518 (ptm-80) cc_final: 0.8110 (ptm-80) REVERT: I 65 MET cc_start: 0.8926 (tpp) cc_final: 0.8646 (tpp) REVERT: I 69 LEU cc_start: 0.8686 (mm) cc_final: 0.8419 (mm) REVERT: J 10 GLN cc_start: 0.8810 (pp30) cc_final: 0.8512 (pp30) REVERT: J 13 ASN cc_start: 0.8435 (m-40) cc_final: 0.8091 (m-40) REVERT: K 16 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7123 (tp30) REVERT: M 5 ARG cc_start: 0.6822 (pmt-80) cc_final: 0.6515 (pmt170) REVERT: N 17 MET cc_start: 0.7461 (ttp) cc_final: 0.7107 (ttp) REVERT: O 42 GLU cc_start: 0.7893 (tp30) cc_final: 0.7629 (tp30) outliers start: 47 outliers final: 31 residues processed: 494 average time/residue: 0.2846 time to fit residues: 188.5798 Evaluate side-chains 446 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 413 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 28 CYS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain O residue 37 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 46 optimal weight: 0.0370 chunk 110 optimal weight: 0.8980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN F 51 HIS ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN K 13 GLN K 71 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 12651 Z= 0.228 Angle : 0.690 10.332 17008 Z= 0.351 Chirality : 0.042 0.200 1873 Planarity : 0.004 0.041 2183 Dihedral : 9.704 154.815 1742 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.19 % Allowed : 19.55 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1531 helix: 1.35 (0.16), residues: 1040 sheet: -1.77 (0.44), residues: 110 loop : -1.89 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 244 HIS 0.023 0.001 HIS K 71 PHE 0.018 0.001 PHE A 81 TYR 0.017 0.001 TYR M 38 ARG 0.008 0.001 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 462 time to evaluate : 1.421 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: A 59 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7739 (tp-100) REVERT: A 123 MET cc_start: 0.7411 (ttp) cc_final: 0.6962 (mmt) REVERT: A 140 GLU cc_start: 0.8319 (pp20) cc_final: 0.7478 (tp30) REVERT: A 185 PHE cc_start: 0.8442 (t80) cc_final: 0.8214 (t80) REVERT: B 241 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8511 (mp) REVERT: C 143 SER cc_start: 0.9256 (t) cc_final: 0.8779 (t) REVERT: C 179 MET cc_start: 0.8269 (mmm) cc_final: 0.8014 (mmm) REVERT: C 214 ASP cc_start: 0.7934 (m-30) cc_final: 0.7495 (m-30) REVERT: C 218 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8267 (tmtt) REVERT: D 17 PHE cc_start: 0.8888 (t80) cc_final: 0.8561 (t80) REVERT: D 18 LEU cc_start: 0.8587 (mt) cc_final: 0.8176 (pp) REVERT: D 53 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8467 (mm) REVERT: E 18 LEU cc_start: 0.8677 (mt) cc_final: 0.8355 (pp) REVERT: E 23 LYS cc_start: 0.9211 (mttp) cc_final: 0.8994 (mttm) REVERT: E 50 GLU cc_start: 0.9420 (tt0) cc_final: 0.9063 (tp30) REVERT: E 55 LYS cc_start: 0.8425 (ptpp) cc_final: 0.8173 (pttm) REVERT: E 58 LYS cc_start: 0.9270 (mtpt) cc_final: 0.8942 (mmmm) REVERT: E 62 ARG cc_start: 0.8888 (ttt180) cc_final: 0.8562 (ttt90) REVERT: E 66 ARG cc_start: 0.8030 (tpt170) cc_final: 0.7727 (tpt90) REVERT: F 20 THR cc_start: 0.9245 (p) cc_final: 0.9032 (t) REVERT: F 35 ASP cc_start: 0.8177 (p0) cc_final: 0.7891 (p0) REVERT: F 42 LYS cc_start: 0.7832 (mtmt) cc_final: 0.7349 (mttt) REVERT: F 50 GLU cc_start: 0.7976 (pt0) cc_final: 0.7521 (tm-30) REVERT: F 62 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.6515 (ttm-80) REVERT: F 66 ARG cc_start: 0.8954 (tpp-160) cc_final: 0.8370 (mpp-170) REVERT: G 20 ASP cc_start: 0.8368 (t70) cc_final: 0.8032 (t0) REVERT: G 21 MET cc_start: 0.8999 (ttp) cc_final: 0.8746 (tmm) REVERT: G 31 ARG cc_start: 0.8984 (ttm-80) cc_final: 0.8460 (ttm-80) REVERT: G 42 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7480 (mm-30) REVERT: H 31 ARG cc_start: 0.8874 (mtm-85) cc_final: 0.8431 (mtm-85) REVERT: H 60 ASP cc_start: 0.9063 (t0) cc_final: 0.8830 (t0) REVERT: I 14 GLU cc_start: 0.8758 (tp30) cc_final: 0.8513 (tp30) REVERT: I 21 MET cc_start: 0.9113 (tmm) cc_final: 0.8278 (tmm) REVERT: I 25 MET cc_start: 0.8754 (ptp) cc_final: 0.8263 (ptp) REVERT: I 60 ASP cc_start: 0.8972 (t0) cc_final: 0.8617 (t0) REVERT: I 63 GLU cc_start: 0.9013 (pt0) cc_final: 0.8730 (pp20) REVERT: I 64 ARG cc_start: 0.8459 (ptm-80) cc_final: 0.8170 (ptm-80) REVERT: J 10 GLN cc_start: 0.8735 (pp30) cc_final: 0.8453 (pp30) REVERT: J 13 ASN cc_start: 0.8407 (m-40) cc_final: 0.8161 (m-40) REVERT: J 77 ARG cc_start: 0.8305 (ttp-110) cc_final: 0.8063 (ttp-110) REVERT: K 16 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7245 (tp30) REVERT: K 58 LYS cc_start: 0.8245 (mttm) cc_final: 0.7883 (mtpp) REVERT: N 17 MET cc_start: 0.7200 (ttp) cc_final: 0.6981 (ttp) outliers start: 69 outliers final: 37 residues processed: 496 average time/residue: 0.2915 time to fit residues: 198.4483 Evaluate side-chains 463 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 424 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 130 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN M 62 HIS N 8 GLN N 23 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12651 Z= 0.329 Angle : 0.718 10.702 17008 Z= 0.367 Chirality : 0.045 0.287 1873 Planarity : 0.004 0.037 2183 Dihedral : 9.532 155.484 1741 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.09 % Allowed : 21.20 % Favored : 72.71 % 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: 0.52 (0.22), residues: 1531 helix: 1.35 (0.16), residues: 1050 sheet: -1.49 (0.46), residues: 107 loop : -1.96 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 244 HIS 0.005 0.001 HIS E 51 PHE 0.027 0.002 PHE A 81 TYR 0.021 0.002 TYR M 38 ARG 0.008 0.001 ARG J 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 446 time to evaluate : 1.521 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: A 72 LYS cc_start: 0.7600 (mtpt) cc_final: 0.7232 (mttp) REVERT: A 123 MET cc_start: 0.7635 (ttp) cc_final: 0.7067 (mmt) REVERT: A 135 MET cc_start: 0.7678 (ttm) cc_final: 0.7469 (ttt) REVERT: A 140 GLU cc_start: 0.8362 (pp20) cc_final: 0.7515 (tp30) REVERT: B 206 MET cc_start: 0.7700 (mmm) cc_final: 0.7285 (mmm) REVERT: B 241 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8477 (mp) REVERT: C 214 ASP cc_start: 0.7927 (m-30) cc_final: 0.7581 (m-30) REVERT: C 218 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8317 (tmtt) REVERT: D 17 PHE cc_start: 0.8944 (t80) cc_final: 0.8600 (t80) REVERT: D 18 LEU cc_start: 0.8576 (mt) cc_final: 0.8265 (pp) REVERT: D 53 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8522 (mm) REVERT: E 17 PHE cc_start: 0.8087 (t80) cc_final: 0.7618 (t80) REVERT: E 18 LEU cc_start: 0.8692 (mt) cc_final: 0.8371 (pp) REVERT: E 50 GLU cc_start: 0.9381 (tt0) cc_final: 0.9005 (tp30) REVERT: E 58 LYS cc_start: 0.9294 (mtpt) cc_final: 0.8958 (mmmm) REVERT: E 66 ARG cc_start: 0.8190 (tpt170) cc_final: 0.7944 (tpt90) REVERT: F 20 THR cc_start: 0.9215 (p) cc_final: 0.8994 (t) REVERT: F 35 ASP cc_start: 0.8380 (p0) cc_final: 0.7949 (p0) REVERT: F 50 GLU cc_start: 0.8142 (pt0) cc_final: 0.7492 (tm-30) REVERT: F 62 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.6933 (ttm-80) REVERT: F 66 ARG cc_start: 0.9055 (tpp-160) cc_final: 0.8244 (mpp-170) REVERT: G 14 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7588 (mm-30) REVERT: G 20 ASP cc_start: 0.8470 (t70) cc_final: 0.8047 (t0) REVERT: G 21 MET cc_start: 0.9018 (ttp) cc_final: 0.8798 (tmm) REVERT: G 31 ARG cc_start: 0.9054 (ttm-80) cc_final: 0.8643 (ttm-80) REVERT: H 31 ARG cc_start: 0.8836 (mtm-85) cc_final: 0.8406 (mtm-85) REVERT: H 60 ASP cc_start: 0.9047 (t0) cc_final: 0.8833 (t0) REVERT: H 65 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7794 (mmp) REVERT: I 14 GLU cc_start: 0.8768 (tp30) cc_final: 0.8531 (tp30) REVERT: I 21 MET cc_start: 0.9106 (tmm) cc_final: 0.8330 (tmm) REVERT: I 25 MET cc_start: 0.8780 (ptp) cc_final: 0.7849 (ptm) REVERT: I 58 TYR cc_start: 0.8761 (t80) cc_final: 0.8368 (t80) REVERT: I 64 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.7758 (ptm-80) REVERT: I 65 MET cc_start: 0.8832 (mmm) cc_final: 0.8488 (mmm) REVERT: I 69 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8206 (tt) REVERT: J 10 GLN cc_start: 0.8773 (pp30) cc_final: 0.8501 (pp30) REVERT: J 13 ASN cc_start: 0.8349 (m-40) cc_final: 0.8075 (m-40) REVERT: J 42 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7255 (p0) REVERT: N 20 ASP cc_start: 0.8040 (t0) cc_final: 0.7836 (t0) REVERT: O 12 GLU cc_start: 0.8245 (pp20) cc_final: 0.8001 (pp20) REVERT: O 16 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7426 (mt-10) outliers start: 81 outliers final: 50 residues processed: 483 average time/residue: 0.2757 time to fit residues: 181.3920 Evaluate side-chains 459 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 404 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 MET Chi-restraints excluded: chain H residue 67 LYS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.7980 chunk 82 optimal weight: 0.0570 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN C 203 GLN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 22 ASN K 71 HIS N 7 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12651 Z= 0.217 Angle : 0.696 11.701 17008 Z= 0.351 Chirality : 0.042 0.296 1873 Planarity : 0.004 0.042 2183 Dihedral : 9.266 156.476 1741 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.04 % Allowed : 22.56 % Favored : 72.41 % 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: 0.79 (0.22), residues: 1531 helix: 1.54 (0.16), residues: 1037 sheet: -1.16 (0.45), residues: 120 loop : -1.75 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 244 HIS 0.014 0.001 HIS E 51 PHE 0.024 0.001 PHE A 81 TYR 0.018 0.001 TYR M 38 ARG 0.006 0.000 ARG N 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 441 time to evaluate : 1.561 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: A 72 LYS cc_start: 0.7579 (mtpt) cc_final: 0.7190 (mttp) REVERT: A 123 MET cc_start: 0.7611 (ttp) cc_final: 0.7042 (mmt) REVERT: A 140 GLU cc_start: 0.8341 (pp20) cc_final: 0.7578 (tp30) REVERT: B 241 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8489 (mp) REVERT: C 214 ASP cc_start: 0.7831 (m-30) cc_final: 0.7501 (m-30) REVERT: C 218 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8309 (tmtt) REVERT: D 17 PHE cc_start: 0.8876 (t80) cc_final: 0.8567 (t80) REVERT: D 23 LYS cc_start: 0.9478 (ttmt) cc_final: 0.9222 (mttt) REVERT: D 45 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9012 (mp0) REVERT: E 17 PHE cc_start: 0.8094 (t80) cc_final: 0.7630 (t80) REVERT: E 18 LEU cc_start: 0.8671 (mt) cc_final: 0.8361 (pp) REVERT: E 23 LYS cc_start: 0.9251 (mttp) cc_final: 0.9038 (mttm) REVERT: E 50 GLU cc_start: 0.9441 (tt0) cc_final: 0.9178 (tp30) REVERT: E 55 LYS cc_start: 0.8479 (ptpp) cc_final: 0.7978 (ptpp) REVERT: E 62 ARG cc_start: 0.8841 (ttt90) cc_final: 0.8549 (ttt90) REVERT: E 66 ARG cc_start: 0.8177 (tpt170) cc_final: 0.7975 (tpt90) REVERT: F 20 THR cc_start: 0.9163 (p) cc_final: 0.8955 (t) REVERT: F 50 GLU cc_start: 0.8044 (pt0) cc_final: 0.7459 (tm-30) REVERT: F 61 GLN cc_start: 0.8541 (mm110) cc_final: 0.8221 (mm110) REVERT: F 62 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.6510 (ttm-80) REVERT: F 66 ARG cc_start: 0.9083 (tpp-160) cc_final: 0.8388 (mpp-170) REVERT: G 20 ASP cc_start: 0.8399 (t70) cc_final: 0.7956 (t0) REVERT: G 22 TYR cc_start: 0.9163 (t80) cc_final: 0.8666 (t80) REVERT: G 31 ARG cc_start: 0.9041 (ttm-80) cc_final: 0.8680 (ttm-80) REVERT: G 42 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7611 (mm-30) REVERT: H 18 MET cc_start: 0.8613 (mmp) cc_final: 0.8344 (mmm) REVERT: H 31 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8421 (mtm-85) REVERT: H 65 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7736 (mmp) REVERT: I 14 GLU cc_start: 0.8816 (tp30) cc_final: 0.8583 (tp30) REVERT: I 21 MET cc_start: 0.9069 (tmm) cc_final: 0.8335 (tmm) REVERT: I 25 MET cc_start: 0.8779 (ptp) cc_final: 0.8009 (ptm) REVERT: I 58 TYR cc_start: 0.8744 (t80) cc_final: 0.8457 (t80) REVERT: I 65 MET cc_start: 0.8751 (mmm) cc_final: 0.8525 (mmm) REVERT: I 69 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8239 (tt) REVERT: J 13 ASN cc_start: 0.8444 (m-40) cc_final: 0.7862 (m-40) REVERT: J 81 ASP cc_start: 0.8462 (t0) cc_final: 0.8260 (t0) REVERT: K 40 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: L 54 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8054 (mm-40) REVERT: O 5 ARG cc_start: 0.8172 (ptt-90) cc_final: 0.7892 (tpp-160) outliers start: 67 outliers final: 40 residues processed: 471 average time/residue: 0.2758 time to fit residues: 176.7353 Evaluate side-chains 461 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 417 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain H residue 65 MET Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 146 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN F 71 HIS ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 71 HIS ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12651 Z= 0.227 Angle : 0.723 12.283 17008 Z= 0.364 Chirality : 0.043 0.311 1873 Planarity : 0.004 0.039 2183 Dihedral : 8.986 157.676 1740 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.34 % Allowed : 22.93 % Favored : 71.73 % 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: 0.80 (0.22), residues: 1531 helix: 1.54 (0.16), residues: 1028 sheet: -1.35 (0.50), residues: 95 loop : -1.59 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 244 HIS 0.021 0.001 HIS K 71 PHE 0.027 0.001 PHE A 81 TYR 0.015 0.001 TYR M 38 ARG 0.008 0.000 ARG M 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 438 time to evaluate : 1.262 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: A 67 GLU cc_start: 0.8162 (pp20) cc_final: 0.7776 (pt0) REVERT: A 72 LYS cc_start: 0.7556 (mtpt) cc_final: 0.7174 (mttp) REVERT: A 123 MET cc_start: 0.7655 (ttp) cc_final: 0.7088 (mmt) REVERT: A 140 GLU cc_start: 0.8334 (pp20) cc_final: 0.7624 (tp30) REVERT: B 111 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7851 (tp30) REVERT: B 241 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8435 (mp) REVERT: C 199 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8766 (t) REVERT: C 214 ASP cc_start: 0.7774 (m-30) cc_final: 0.7515 (m-30) REVERT: D 23 LYS cc_start: 0.9480 (ttmt) cc_final: 0.9220 (mttt) REVERT: E 18 LEU cc_start: 0.8688 (mt) cc_final: 0.8335 (pp) REVERT: E 50 GLU cc_start: 0.9422 (tt0) cc_final: 0.9139 (tp30) REVERT: E 58 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8789 (mtmt) REVERT: F 27 THR cc_start: 0.8698 (m) cc_final: 0.8211 (t) REVERT: F 31 ASP cc_start: 0.8461 (m-30) cc_final: 0.8032 (m-30) REVERT: G 14 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7524 (mm-30) REVERT: G 20 ASP cc_start: 0.8362 (t70) cc_final: 0.7886 (t0) REVERT: G 31 ARG cc_start: 0.9007 (ttm-80) cc_final: 0.8674 (ttm-80) REVERT: H 31 ARG cc_start: 0.8789 (mtm-85) cc_final: 0.8398 (mtm-85) REVERT: I 14 GLU cc_start: 0.8829 (tp30) cc_final: 0.8585 (tp30) REVERT: I 21 MET cc_start: 0.9074 (tmm) cc_final: 0.8220 (tmm) REVERT: I 25 MET cc_start: 0.8849 (ptp) cc_final: 0.7861 (ptm) REVERT: I 58 TYR cc_start: 0.8700 (t80) cc_final: 0.8344 (t80) REVERT: I 64 ARG cc_start: 0.8457 (ptm-80) cc_final: 0.8161 (ptm-80) REVERT: I 65 MET cc_start: 0.8759 (mmm) cc_final: 0.8504 (tpp) REVERT: J 9 GLN cc_start: 0.8504 (tp40) cc_final: 0.7813 (tp40) REVERT: J 10 GLN cc_start: 0.8704 (pp30) cc_final: 0.8329 (pp30) REVERT: J 13 ASN cc_start: 0.8355 (m-40) cc_final: 0.7943 (m-40) REVERT: J 81 ASP cc_start: 0.8515 (t0) cc_final: 0.8240 (t0) REVERT: K 40 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: L 54 GLN cc_start: 0.8280 (mm-40) cc_final: 0.8076 (mm-40) REVERT: L 76 GLU cc_start: 0.8015 (pp20) cc_final: 0.7781 (pp20) REVERT: N 17 MET cc_start: 0.7579 (tmm) cc_final: 0.7194 (ttp) outliers start: 71 outliers final: 47 residues processed: 471 average time/residue: 0.2773 time to fit residues: 177.0032 Evaluate side-chains 461 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 411 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 0.0980 chunk 67 optimal weight: 0.0030 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN F 71 HIS I 62 HIS K 13 GLN ** L 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12651 Z= 0.215 Angle : 0.757 13.267 17008 Z= 0.377 Chirality : 0.043 0.312 1873 Planarity : 0.004 0.040 2183 Dihedral : 8.756 159.850 1740 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.26 % Allowed : 24.66 % Favored : 70.08 % 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: 0.79 (0.22), residues: 1531 helix: 1.50 (0.16), residues: 1031 sheet: -1.27 (0.50), residues: 95 loop : -1.57 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 244 HIS 0.013 0.001 HIS E 51 PHE 0.028 0.001 PHE A 81 TYR 0.016 0.001 TYR M 38 ARG 0.007 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 453 time to evaluate : 1.419 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: A 60 LYS cc_start: 0.8123 (ptpp) cc_final: 0.7877 (ptpp) REVERT: A 64 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7713 (ttmm) REVERT: A 67 GLU cc_start: 0.8152 (pp20) cc_final: 0.7827 (pt0) REVERT: A 72 LYS cc_start: 0.7627 (mtpt) cc_final: 0.7277 (mttp) REVERT: A 123 MET cc_start: 0.7699 (ttp) cc_final: 0.7128 (mmt) REVERT: B 107 LYS cc_start: 0.8036 (mttm) cc_final: 0.7659 (mttm) REVERT: B 111 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7826 (tp30) REVERT: B 163 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8770 (t) REVERT: B 241 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8431 (mp) REVERT: C 85 GLU cc_start: 0.8003 (tp30) cc_final: 0.7606 (mm-30) REVERT: C 199 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8713 (t) REVERT: C 214 ASP cc_start: 0.7687 (m-30) cc_final: 0.7443 (m-30) REVERT: D 17 PHE cc_start: 0.8875 (t80) cc_final: 0.8655 (t80) REVERT: D 23 LYS cc_start: 0.9488 (ttmt) cc_final: 0.9239 (mttt) REVERT: E 17 PHE cc_start: 0.7980 (t80) cc_final: 0.7280 (t80) REVERT: E 18 LEU cc_start: 0.8595 (mt) cc_final: 0.8317 (pp) REVERT: E 50 GLU cc_start: 0.9394 (tt0) cc_final: 0.9128 (tp30) REVERT: E 55 LYS cc_start: 0.8356 (ptpp) cc_final: 0.7996 (pttt) REVERT: E 58 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8793 (mtmt) REVERT: E 62 ARG cc_start: 0.8790 (ttt90) cc_final: 0.8466 (ttt90) REVERT: F 61 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8184 (mm110) REVERT: F 62 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.6664 (ttm-80) REVERT: F 66 ARG cc_start: 0.8897 (tpp-160) cc_final: 0.8096 (mpp-170) REVERT: G 17 MET cc_start: 0.8257 (ppp) cc_final: 0.7425 (ppp) REVERT: G 20 ASP cc_start: 0.8362 (t70) cc_final: 0.7929 (t0) REVERT: G 31 ARG cc_start: 0.8969 (ttm-80) cc_final: 0.8682 (ttm-80) REVERT: H 18 MET cc_start: 0.8608 (mmp) cc_final: 0.8367 (mmm) REVERT: H 31 ARG cc_start: 0.8795 (mtm-85) cc_final: 0.8412 (mtm-85) REVERT: I 14 GLU cc_start: 0.8800 (tp30) cc_final: 0.8562 (tp30) REVERT: I 21 MET cc_start: 0.9089 (tmm) cc_final: 0.8174 (tmm) REVERT: I 25 MET cc_start: 0.8799 (ptp) cc_final: 0.7852 (ptm) REVERT: I 58 TYR cc_start: 0.8677 (t80) cc_final: 0.8380 (t80) REVERT: I 64 ARG cc_start: 0.8424 (ptm-80) cc_final: 0.8122 (ptm-80) REVERT: I 69 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8296 (tp) REVERT: J 10 GLN cc_start: 0.8717 (pp30) cc_final: 0.8370 (pp30) REVERT: J 13 ASN cc_start: 0.8446 (m-40) cc_final: 0.7924 (m-40) REVERT: J 31 ARG cc_start: 0.8199 (ptp-170) cc_final: 0.7937 (ptp-170) REVERT: J 82 TYR cc_start: 0.5496 (t80) cc_final: 0.5266 (m-10) REVERT: K 40 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: L 76 GLU cc_start: 0.8030 (pp20) cc_final: 0.7685 (pp20) REVERT: N 17 MET cc_start: 0.7489 (tmm) cc_final: 0.7241 (ttp) REVERT: N 20 ASP cc_start: 0.7976 (t0) cc_final: 0.7737 (t0) outliers start: 70 outliers final: 50 residues processed: 484 average time/residue: 0.2680 time to fit residues: 176.5614 Evaluate side-chains 481 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 426 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain M residue 50 CYS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN F 71 HIS L 54 GLN ** L 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12651 Z= 0.243 Angle : 0.779 13.892 17008 Z= 0.391 Chirality : 0.045 0.337 1873 Planarity : 0.004 0.035 2183 Dihedral : 8.695 161.065 1740 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.71 % Allowed : 25.04 % Favored : 69.25 % 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: 0.81 (0.22), residues: 1531 helix: 1.51 (0.16), residues: 1033 sheet: -1.32 (0.50), residues: 96 loop : -1.52 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 244 HIS 0.014 0.001 HIS E 51 PHE 0.029 0.001 PHE E 29 TYR 0.026 0.002 TYR J 67 ARG 0.006 0.001 ARG N 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 439 time to evaluate : 1.452 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: A 67 GLU cc_start: 0.8170 (pp20) cc_final: 0.7825 (pt0) REVERT: A 72 LYS cc_start: 0.7718 (mtpt) cc_final: 0.7398 (mttp) REVERT: A 123 MET cc_start: 0.7639 (ttp) cc_final: 0.7038 (mmt) REVERT: A 182 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8064 (t80) REVERT: B 107 LYS cc_start: 0.8110 (mttm) cc_final: 0.7719 (mttm) REVERT: B 191 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7652 (p0) REVERT: B 241 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8406 (mp) REVERT: C 85 GLU cc_start: 0.8001 (tp30) cc_final: 0.7576 (mm-30) REVERT: C 135 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: C 199 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8722 (t) REVERT: C 214 ASP cc_start: 0.7700 (m-30) cc_final: 0.7456 (m-30) REVERT: D 17 PHE cc_start: 0.8896 (t80) cc_final: 0.8684 (t80) REVERT: D 23 LYS cc_start: 0.9492 (ttmt) cc_final: 0.9263 (mttt) REVERT: D 50 GLU cc_start: 0.8503 (tt0) cc_final: 0.8018 (tm-30) REVERT: D 54 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: E 18 LEU cc_start: 0.8599 (mt) cc_final: 0.8239 (pp) REVERT: E 50 GLU cc_start: 0.9361 (tt0) cc_final: 0.9121 (tp30) REVERT: E 55 LYS cc_start: 0.8401 (ptpp) cc_final: 0.8201 (ptpp) REVERT: E 58 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8666 (mtmt) REVERT: F 31 ASP cc_start: 0.8542 (m-30) cc_final: 0.8134 (m-30) REVERT: F 61 GLN cc_start: 0.8686 (mm110) cc_final: 0.8318 (mm110) REVERT: G 14 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7923 (mm-30) REVERT: G 20 ASP cc_start: 0.8167 (t70) cc_final: 0.7745 (t0) REVERT: G 31 ARG cc_start: 0.8971 (ttm-80) cc_final: 0.8679 (ttm-80) REVERT: H 31 ARG cc_start: 0.8787 (mtm-85) cc_final: 0.8371 (mtm-85) REVERT: I 14 GLU cc_start: 0.8739 (tp30) cc_final: 0.8495 (tp30) REVERT: I 21 MET cc_start: 0.9096 (tmm) cc_final: 0.8280 (tmm) REVERT: I 25 MET cc_start: 0.8816 (ptp) cc_final: 0.8085 (ptm) REVERT: I 58 TYR cc_start: 0.8742 (t80) cc_final: 0.8400 (t80) REVERT: I 64 ARG cc_start: 0.8419 (ptm-80) cc_final: 0.7860 (ptm-80) REVERT: J 10 GLN cc_start: 0.8730 (pp30) cc_final: 0.8342 (pp30) REVERT: J 31 ARG cc_start: 0.8218 (ptp-170) cc_final: 0.7940 (ptp-170) REVERT: J 82 TYR cc_start: 0.5328 (t80) cc_final: 0.4997 (m-10) REVERT: K 21 TYR cc_start: 0.8949 (t80) cc_final: 0.8735 (t80) REVERT: K 40 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7848 (pm20) REVERT: N 20 ASP cc_start: 0.8098 (t0) cc_final: 0.7843 (t0) REVERT: O 42 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6626 (mm-30) outliers start: 76 outliers final: 59 residues processed: 477 average time/residue: 0.2751 time to fit residues: 179.4478 Evaluate side-chains 488 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 421 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain M residue 50 CYS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 0.0770 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 143 optimal weight: 0.5980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** L 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12651 Z= 0.232 Angle : 0.801 17.563 17008 Z= 0.403 Chirality : 0.046 0.318 1873 Planarity : 0.004 0.036 2183 Dihedral : 8.601 162.693 1738 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.26 % Allowed : 25.94 % Favored : 68.80 % 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: 0.83 (0.22), residues: 1531 helix: 1.48 (0.16), residues: 1033 sheet: -1.25 (0.50), residues: 96 loop : -1.38 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 244 HIS 0.015 0.001 HIS E 51 PHE 0.028 0.001 PHE E 29 TYR 0.022 0.002 TYR J 67 ARG 0.008 0.001 ARG J 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 447 time to evaluate : 1.378 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: A 67 GLU cc_start: 0.8169 (pp20) cc_final: 0.7875 (pt0) REVERT: A 72 LYS cc_start: 0.7677 (mtpt) cc_final: 0.7340 (mttp) REVERT: A 123 MET cc_start: 0.7543 (ttp) cc_final: 0.6963 (mmt) REVERT: A 135 MET cc_start: 0.7985 (ttm) cc_final: 0.7723 (ttt) REVERT: A 182 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8075 (t80) REVERT: B 107 LYS cc_start: 0.8071 (mttm) cc_final: 0.7703 (mttm) REVERT: B 191 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7687 (p0) REVERT: B 241 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8359 (mp) REVERT: C 85 GLU cc_start: 0.7884 (tp30) cc_final: 0.7510 (mm-30) REVERT: C 135 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: C 199 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8707 (t) REVERT: C 214 ASP cc_start: 0.7630 (m-30) cc_final: 0.7403 (m-30) REVERT: C 224 ASP cc_start: 0.8379 (t70) cc_final: 0.7590 (t70) REVERT: C 228 ASP cc_start: 0.8448 (m-30) cc_final: 0.8028 (m-30) REVERT: D 17 PHE cc_start: 0.8886 (t80) cc_final: 0.8680 (t80) REVERT: D 23 LYS cc_start: 0.9492 (ttmt) cc_final: 0.9269 (mttt) REVERT: E 18 LEU cc_start: 0.8560 (mt) cc_final: 0.8160 (pp) REVERT: E 50 GLU cc_start: 0.9385 (tt0) cc_final: 0.9134 (tp30) REVERT: E 55 LYS cc_start: 0.8391 (ptpp) cc_final: 0.7908 (pttt) REVERT: E 58 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8682 (mtmt) REVERT: F 31 ASP cc_start: 0.8562 (m-30) cc_final: 0.8106 (m-30) REVERT: F 62 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.7893 (ttm-80) REVERT: G 20 ASP cc_start: 0.8240 (t70) cc_final: 0.7870 (t0) REVERT: G 31 ARG cc_start: 0.8951 (ttm-80) cc_final: 0.8693 (ttm-80) REVERT: I 14 GLU cc_start: 0.8740 (tp30) cc_final: 0.8499 (tp30) REVERT: I 21 MET cc_start: 0.9090 (tmm) cc_final: 0.8279 (tmm) REVERT: I 25 MET cc_start: 0.8827 (ptp) cc_final: 0.8117 (ptm) REVERT: I 58 TYR cc_start: 0.8718 (t80) cc_final: 0.8411 (t80) REVERT: I 64 ARG cc_start: 0.8157 (ptm-80) cc_final: 0.7584 (ptm-80) REVERT: I 65 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7672 (mmt) REVERT: I 69 LEU cc_start: 0.8547 (mm) cc_final: 0.8233 (tt) REVERT: J 9 GLN cc_start: 0.8352 (tp40) cc_final: 0.8125 (tp40) REVERT: J 23 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.8358 (mtm110) REVERT: J 31 ARG cc_start: 0.8156 (ptp-170) cc_final: 0.7904 (ptp-170) REVERT: J 81 ASP cc_start: 0.8071 (t0) cc_final: 0.7858 (t0) REVERT: J 82 TYR cc_start: 0.5311 (t80) cc_final: 0.4872 (m-10) REVERT: K 40 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: O 42 GLU cc_start: 0.7197 (tp30) cc_final: 0.6836 (mm-30) outliers start: 70 outliers final: 53 residues processed: 482 average time/residue: 0.2839 time to fit residues: 186.5691 Evaluate side-chains 490 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 430 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 65 MET Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain M residue 50 CYS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 119 optimal weight: 0.0000 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN L 68 GLN O 8 GLN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12651 Z= 0.281 Angle : 0.844 15.191 17008 Z= 0.424 Chirality : 0.047 0.307 1873 Planarity : 0.004 0.037 2183 Dihedral : 8.594 163.011 1738 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.49 % Allowed : 26.17 % Favored : 68.35 % 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: 0.82 (0.22), residues: 1531 helix: 1.46 (0.16), residues: 1032 sheet: -1.23 (0.51), residues: 95 loop : -1.36 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 244 HIS 0.018 0.001 HIS E 51 PHE 0.029 0.001 PHE A 81 TYR 0.025 0.002 TYR J 67 ARG 0.009 0.001 ARG H 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 428 time to evaluate : 1.486 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: A 72 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7319 (mttp) REVERT: A 123 MET cc_start: 0.7687 (ttp) cc_final: 0.7072 (mmt) REVERT: A 135 MET cc_start: 0.7881 (ttm) cc_final: 0.7656 (ttt) REVERT: A 182 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8185 (t80) REVERT: B 107 LYS cc_start: 0.8116 (mttm) cc_final: 0.7716 (mttm) REVERT: B 191 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7603 (p0) REVERT: B 241 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8354 (mp) REVERT: C 85 GLU cc_start: 0.7823 (tp30) cc_final: 0.7458 (mm-30) REVERT: C 135 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: C 199 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8687 (t) REVERT: C 214 ASP cc_start: 0.7603 (m-30) cc_final: 0.7345 (m-30) REVERT: C 217 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7869 (p90) REVERT: C 224 ASP cc_start: 0.8366 (t70) cc_final: 0.7570 (t70) REVERT: C 228 ASP cc_start: 0.8340 (m-30) cc_final: 0.7983 (m-30) REVERT: D 23 LYS cc_start: 0.9501 (ttmt) cc_final: 0.9242 (mttt) REVERT: D 26 GLU cc_start: 0.8451 (tt0) cc_final: 0.8144 (mt-10) REVERT: E 18 LEU cc_start: 0.8541 (mt) cc_final: 0.8178 (pp) REVERT: E 50 GLU cc_start: 0.9389 (tt0) cc_final: 0.9153 (tp30) REVERT: E 53 LEU cc_start: 0.9341 (mp) cc_final: 0.8889 (mp) REVERT: E 58 LYS cc_start: 0.8951 (mtmt) cc_final: 0.8737 (mtmt) REVERT: F 31 ASP cc_start: 0.8571 (m-30) cc_final: 0.8090 (m-30) REVERT: F 62 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7949 (ttm-80) REVERT: G 20 ASP cc_start: 0.8264 (t70) cc_final: 0.7857 (t0) REVERT: G 31 ARG cc_start: 0.8993 (ttm-80) cc_final: 0.8704 (ttm-80) REVERT: H 53 ARG cc_start: 0.8250 (mmt180) cc_final: 0.8033 (mmt180) REVERT: I 14 GLU cc_start: 0.8739 (tp30) cc_final: 0.8490 (tp30) REVERT: I 21 MET cc_start: 0.9103 (tmm) cc_final: 0.8274 (tmm) REVERT: I 25 MET cc_start: 0.8816 (ptp) cc_final: 0.8092 (ptm) REVERT: I 58 TYR cc_start: 0.8760 (t80) cc_final: 0.8427 (t80) REVERT: I 69 LEU cc_start: 0.8560 (mm) cc_final: 0.8296 (tt) REVERT: J 23 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8365 (mtm110) REVERT: J 31 ARG cc_start: 0.8194 (ptp-170) cc_final: 0.7912 (ptp-170) REVERT: J 82 TYR cc_start: 0.5466 (t80) cc_final: 0.4938 (m-10) REVERT: K 40 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: M 63 GLU cc_start: 0.7630 (pm20) cc_final: 0.7283 (pm20) REVERT: O 42 GLU cc_start: 0.7261 (tp30) cc_final: 0.6891 (mm-30) outliers start: 73 outliers final: 58 residues processed: 467 average time/residue: 0.2765 time to fit residues: 175.7258 Evaluate side-chains 480 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 415 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 14 PHE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain H residue 67 LYS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain M residue 50 CYS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 50 optimal weight: 50.0000 chunk 123 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN L 54 GLN L 68 GLN ** O 30 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 = 0.3821 r_free = 0.3821 target = 0.117591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.092466 restraints weight = 29669.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.091366 restraints weight = 21265.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092270 restraints weight = 23109.931| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12651 Z= 0.283 Angle : 0.830 14.458 17008 Z= 0.424 Chirality : 0.047 0.335 1873 Planarity : 0.004 0.035 2183 Dihedral : 8.577 163.373 1738 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.19 % Allowed : 26.92 % Favored : 67.89 % 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: 0.79 (0.22), residues: 1531 helix: 1.43 (0.16), residues: 1031 sheet: -1.23 (0.52), residues: 93 loop : -1.35 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 244 HIS 0.016 0.001 HIS E 51 PHE 0.030 0.002 PHE E 29 TYR 0.026 0.002 TYR J 67 ARG 0.007 0.001 ARG J 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3483.31 seconds wall clock time: 64 minutes 12.73 seconds (3852.73 seconds total)