Starting phenix.real_space_refine on Thu Sep 26 07:44:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/09_2024/7cgp_9958.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/09_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_9958/09_2024/7cgp_9958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/09_2024/7cgp_9958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/09_2024/7cgp_9958.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgp_9958/09_2024/7cgp_9958.cif" } 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. Time to flip 46 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.09, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.6 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... Secondary structure from input PDB file: 56 helices and 4 sheets defined 72.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 4.342A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 93 removed outlier: 3.878A pdb=" N LYS A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 148 Processing helix chain 'A' and resid 151 through 171 removed outlier: 3.990A pdb=" N SER A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 193 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 24 through 51 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.504A pdb=" N LEU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.883A pdb=" N HIS B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) 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 221 Processing helix chain 'B' and resid 227 through 243 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) removed outlier: 3.802A pdb=" N GLU B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.720A pdb=" N ARG B 351 " --> pdb=" O THR B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 415 Processing helix chain 'C' and resid 22 through 55 Processing helix chain 'C' and resid 58 through 75 Processing helix chain 'C' and resid 78 through 97 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) removed outlier: 4.067A pdb=" N LEU C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 119 removed outlier: 3.831A pdb=" N ARG C 119 " --> pdb=" O TRP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.514A pdb=" N ARG C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Proline residue: C 160 - end of helix removed outlier: 3.657A pdb=" N VAL C 163 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.855A pdb=" N LEU C 190 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS C 191 " --> pdb=" O GLU C 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 191' Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.620A pdb=" N LEU C 196 " --> pdb=" O PRO C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.516A pdb=" N ARG C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 244 Processing helix chain 'D' and resid 14 through 32 Processing helix chain 'D' and resid 42 through 76 removed outlier: 3.758A pdb=" N THR D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) 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 13 through 30 removed outlier: 3.926A pdb=" N PHE E 17 " --> pdb=" O GLN E 13 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 75 Processing helix chain 'F' and resid 14 through 33 Processing helix chain 'F' and resid 42 through 75 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 33 removed outlier: 3.621A pdb=" N MET G 21 " --> pdb=" O MET G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 75 removed outlier: 3.716A pdb=" N SER G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) 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 34 Processing helix chain 'H' and resid 44 through 75 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 34 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 44 through 49 removed outlier: 3.595A pdb=" N VAL I 49 " --> pdb=" O LYS I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 73 removed outlier: 3.661A pdb=" N ARG I 53 " --> pdb=" O VAL I 49 " (cutoff:3.500A) 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 31 Processing helix chain 'J' and resid 42 through 85 Proline residue: J 72 - end of helix Processing helix chain 'K' and resid 9 through 32 Processing helix chain 'K' and resid 45 through 77 removed outlier: 3.812A pdb=" N SER K 49 " --> pdb=" O GLU K 45 " (cutoff:3.500A) 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) removed outlier: 3.871A pdb=" N ALA K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 33 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 43 through 82 removed outlier: 4.397A pdb=" N SER L 49 " --> pdb=" O GLU L 45 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 34 Processing helix chain 'M' and resid 45 through 75 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 34 removed outlier: 3.593A pdb=" N CYS N 33 " --> pdb=" O CYS N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 59 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 60 through 73 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 34 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 44 through 77 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) removed outlier: 3.502A pdb=" N GLU O 77 " --> pdb=" O SER O 73 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.227A pdb=" N THR B 64 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA B 122 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE B 66 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 119 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE B 152 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 121 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 205 removed outlier: 6.213A pdb=" N VAL B 188 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 404 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU B 190 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 402 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 367 through 368 Processing sheet with id=AA4, first strand: chain 'C' and resid 125 through 126 876 hydrogen bonds defined for protein. 2592 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: 3.53 Time building geometry restraints manager: 3.75 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: 0.00 - 2.03: 16624 2.03 - 4.07: 364 4.07 - 6.10: 19 6.10 - 8.14: 0 8.14 - 10.17: 1 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: 75 2.46 - 3.07: 9289 3.07 - 3.68: 18702 3.68 - 4.29: 25669 4.29 - 4.90: 42681 Nonbonded interactions: 96416 Sorted by model distance: nonbonded pdb=" OH TYR D 70 " pdb=" OE2 GLU G 63 " model vdw 1.852 3.040 nonbonded pdb=" O ILE B 335 " pdb=" OG1 THR B 363 " model vdw 1.882 3.040 nonbonded pdb=" NE2 GLN K 74 " pdb=" OE2 GLU O 63 " model vdw 1.951 3.120 nonbonded pdb=" OE2 GLU A 144 " pdb=" OG SER A 150 " model vdw 2.036 3.040 nonbonded pdb=" OH TYR F 21 " pdb=" O HIS G 62 " model vdw 2.068 3.040 ... (remaining 96411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.450 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- 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= 0.405 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 : 1.426 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: 0.3034 time to fit residues: 235.3519 Evaluate side-chains 426 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 421 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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: 0.8980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 118 optimal weight: 0.0060 chunk 45 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN E 54 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 HIS J 9 GLN K 71 HIS L 71 HIS L 74 GLN M 30 HIS N 8 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 12651 Z= 0.270 Angle : 0.754 12.076 17008 Z= 0.389 Chirality : 0.045 0.299 1873 Planarity : 0.005 0.053 2183 Dihedral : 10.289 155.332 1744 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.38 % Allowed : 17.82 % Favored : 78.80 % 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: -0.34 (0.21), residues: 1531 helix: 0.80 (0.16), residues: 1056 sheet: -2.16 (0.41), residues: 114 loop : -2.54 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 28 HIS 0.011 0.001 HIS I 62 PHE 0.023 0.002 PHE A 81 TYR 0.019 0.002 TYR C 124 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 526 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 481 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7342 (ttp) cc_final: 0.7008 (mmt) REVERT: A 140 GLU cc_start: 0.8337 (pp20) cc_final: 0.7421 (tp30) REVERT: A 185 PHE cc_start: 0.8413 (t80) cc_final: 0.8163 (t80) REVERT: B 241 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 329 ASP cc_start: 0.6456 (p0) cc_final: 0.5968 (p0) REVERT: B 390 TYR cc_start: 0.8230 (m-80) cc_final: 0.7960 (m-10) REVERT: C 76 LEU cc_start: 0.6699 (tp) cc_final: 0.6430 (pp) REVERT: C 134 TYR cc_start: 0.8908 (p90) cc_final: 0.8647 (p90) REVERT: C 143 SER cc_start: 0.9068 (t) cc_final: 0.8573 (t) REVERT: C 214 ASP cc_start: 0.7965 (m-30) cc_final: 0.7673 (m-30) REVERT: C 218 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8136 (tmtt) REVERT: E 18 LEU cc_start: 0.8656 (mt) cc_final: 0.8435 (pp) REVERT: E 23 LYS cc_start: 0.9207 (mttp) cc_final: 0.8996 (mttm) REVERT: E 51 HIS cc_start: 0.8358 (m170) cc_final: 0.8066 (m170) REVERT: E 58 LYS cc_start: 0.9226 (mtpt) cc_final: 0.8980 (mmmm) REVERT: E 62 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8555 (ttt180) REVERT: F 20 THR cc_start: 0.9247 (p) cc_final: 0.9024 (t) REVERT: F 62 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.6491 (ttm-80) REVERT: F 66 ARG cc_start: 0.8924 (tpp-160) cc_final: 0.8315 (mpp-170) REVERT: G 13 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.7825 (tp) REVERT: G 20 ASP cc_start: 0.8336 (t70) cc_final: 0.8041 (t0) REVERT: G 31 ARG cc_start: 0.9142 (ttm-80) cc_final: 0.8552 (ttm-80) REVERT: G 42 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7327 (mm-30) REVERT: H 25 MET cc_start: 0.9057 (ptm) cc_final: 0.8818 (ptm) REVERT: H 49 VAL cc_start: 0.9127 (t) cc_final: 0.8866 (p) REVERT: H 64 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8416 (ttm-80) REVERT: I 14 GLU cc_start: 0.8770 (tp30) cc_final: 0.8427 (tp30) REVERT: I 21 MET cc_start: 0.9135 (tmm) cc_final: 0.8279 (tmm) REVERT: I 25 MET cc_start: 0.8666 (ptp) cc_final: 0.7598 (ptm) REVERT: I 58 TYR cc_start: 0.8703 (t80) cc_final: 0.8018 (t80) REVERT: I 60 ASP cc_start: 0.9008 (t0) cc_final: 0.8660 (t0) REVERT: I 63 GLU cc_start: 0.9011 (pt0) cc_final: 0.8656 (pp20) REVERT: I 64 ARG cc_start: 0.8544 (ptm-80) cc_final: 0.8020 (ptm-80) REVERT: J 9 GLN cc_start: 0.8577 (tp-100) cc_final: 0.7978 (tp40) REVERT: J 10 GLN cc_start: 0.8830 (pp30) cc_final: 0.8572 (pp30) REVERT: K 16 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7149 (tp30) REVERT: L 69 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7533 (tm-30) REVERT: M 5 ARG cc_start: 0.6814 (pmt-80) cc_final: 0.6577 (pmt170) REVERT: O 16 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7039 (mt-10) outliers start: 45 outliers final: 24 residues processed: 493 average time/residue: 0.2924 time to fit residues: 191.9688 Evaluate side-chains 438 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 411 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 226 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 408 CYS 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 46 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 62 ARG 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 52 ASP Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain K residue 9 ASP 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 N residue 31 ARG 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: 0.9980 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 C 203 GLN E 54 GLN F 51 HIS ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 ASN L 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12651 Z= 0.244 Angle : 0.728 11.943 17008 Z= 0.376 Chirality : 0.043 0.216 1873 Planarity : 0.004 0.038 2183 Dihedral : 9.710 154.430 1740 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.89 % Allowed : 20.15 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.22), residues: 1531 helix: 1.25 (0.16), residues: 1066 sheet: -1.59 (0.45), residues: 109 loop : -2.12 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 244 HIS 0.019 0.001 HIS K 71 PHE 0.018 0.001 PHE A 81 TYR 0.018 0.002 TYR L 70 ARG 0.007 0.001 ARG J 23 *********************** 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 526 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 461 time to evaluate : 1.424 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: A 59 GLN cc_start: 0.8032 (tp-100) cc_final: 0.7790 (tp-100) REVERT: A 123 MET cc_start: 0.7520 (ttp) cc_final: 0.7131 (mmt) REVERT: A 140 GLU cc_start: 0.8311 (pp20) cc_final: 0.7568 (tp30) REVERT: B 107 LYS cc_start: 0.8336 (mtmm) cc_final: 0.8090 (mttm) REVERT: B 113 MET cc_start: 0.8176 (ttm) cc_final: 0.7956 (ttm) REVERT: B 241 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8501 (mp) REVERT: B 329 ASP cc_start: 0.6565 (p0) cc_final: 0.6002 (p0) REVERT: B 359 HIS cc_start: 0.6924 (m-70) cc_final: 0.6716 (m-70) REVERT: B 390 TYR cc_start: 0.8427 (m-80) cc_final: 0.8183 (m-10) REVERT: C 134 TYR cc_start: 0.8942 (p90) cc_final: 0.8677 (p90) REVERT: C 143 SER cc_start: 0.9163 (t) cc_final: 0.8692 (t) REVERT: C 218 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8280 (tmtt) REVERT: D 17 PHE cc_start: 0.8902 (t80) cc_final: 0.8590 (t80) REVERT: D 39 ARG cc_start: 0.8530 (ttp80) cc_final: 0.8126 (tpt90) REVERT: D 53 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8319 (mm) REVERT: E 18 LEU cc_start: 0.8680 (mt) cc_final: 0.8321 (pp) REVERT: E 50 GLU cc_start: 0.9410 (tt0) cc_final: 0.9005 (tp30) REVERT: E 58 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8946 (mmmm) REVERT: E 62 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8397 (ttt90) REVERT: F 35 ASP cc_start: 0.8334 (p0) cc_final: 0.7970 (p0) REVERT: F 50 GLU cc_start: 0.7909 (pt0) cc_final: 0.7515 (tm-30) REVERT: F 62 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.6571 (ttm-80) REVERT: F 66 ARG cc_start: 0.8922 (tpp-160) cc_final: 0.8303 (mpp-170) REVERT: G 20 ASP cc_start: 0.8415 (t70) cc_final: 0.8109 (t0) REVERT: G 21 MET cc_start: 0.8979 (ttp) cc_final: 0.8707 (tmm) REVERT: G 31 ARG cc_start: 0.9123 (ttm-80) cc_final: 0.8701 (ttm-80) REVERT: G 42 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7415 (mm-30) REVERT: H 31 ARG cc_start: 0.8955 (mtm-85) cc_final: 0.8486 (mtm-85) REVERT: H 60 ASP cc_start: 0.8988 (t0) cc_final: 0.8698 (t0) REVERT: I 14 GLU cc_start: 0.8755 (tp30) cc_final: 0.8515 (tp30) REVERT: I 21 MET cc_start: 0.9093 (tmm) cc_final: 0.8294 (tmm) REVERT: I 25 MET cc_start: 0.8740 (ptp) cc_final: 0.8223 (ptp) REVERT: J 9 GLN cc_start: 0.8580 (tp-100) cc_final: 0.8371 (tp40) REVERT: J 74 LEU cc_start: 0.8757 (tp) cc_final: 0.8406 (tp) REVERT: K 40 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: L 69 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7775 (tm-30) REVERT: N 14 GLU cc_start: 0.5833 (mm-30) cc_final: 0.5446 (mm-30) REVERT: N 17 MET cc_start: 0.7340 (ttp) cc_final: 0.7014 (ttp) outliers start: 65 outliers final: 28 residues processed: 495 average time/residue: 0.2767 time to fit residues: 184.7912 Evaluate side-chains 436 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 404 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 149 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 241 LEU 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 46 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR 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 72 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain L residue 28 CYS Chi-restraints excluded: chain L residue 73 GLN Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 37 HIS 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: 0.8980 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 203 GLN E 51 HIS ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 22 ASN K 71 HIS N 8 GLN O 37 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12651 Z= 0.234 Angle : 0.748 11.733 17008 Z= 0.381 Chirality : 0.043 0.296 1873 Planarity : 0.004 0.037 2183 Dihedral : 9.488 154.651 1739 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.66 % Allowed : 22.56 % Favored : 72.78 % 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: 0.69 (0.22), residues: 1531 helix: 1.47 (0.16), residues: 1055 sheet: -1.29 (0.46), residues: 111 loop : -1.96 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 244 HIS 0.009 0.001 HIS F 71 PHE 0.025 0.001 PHE A 81 TYR 0.021 0.001 TYR M 38 ARG 0.007 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 506 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 444 time to evaluate : 1.393 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: A 59 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7733 (tp-100) REVERT: A 123 MET cc_start: 0.7547 (ttp) cc_final: 0.7126 (mmt) REVERT: A 140 GLU cc_start: 0.8316 (pp20) cc_final: 0.7582 (tp30) REVERT: B 241 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8466 (mp) REVERT: B 390 TYR cc_start: 0.8459 (m-80) cc_final: 0.8244 (m-10) REVERT: C 143 SER cc_start: 0.9227 (t) cc_final: 0.8765 (t) REVERT: C 218 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8300 (tmtt) REVERT: D 17 PHE cc_start: 0.8889 (t80) cc_final: 0.8598 (t80) REVERT: D 35 ASP cc_start: 0.8309 (p0) cc_final: 0.8038 (p0) REVERT: D 39 ARG cc_start: 0.8600 (ttp80) cc_final: 0.8240 (tpt90) REVERT: E 18 LEU cc_start: 0.8732 (mt) cc_final: 0.8425 (pp) REVERT: E 50 GLU cc_start: 0.9348 (tt0) cc_final: 0.9017 (tp30) REVERT: E 55 LYS cc_start: 0.8463 (ptpp) cc_final: 0.8180 (ptpp) REVERT: E 62 ARG cc_start: 0.8756 (ttt90) cc_final: 0.8353 (ttt90) REVERT: F 42 LYS cc_start: 0.7711 (mttt) cc_final: 0.7147 (mttt) REVERT: F 50 GLU cc_start: 0.8050 (pt0) cc_final: 0.7514 (tm-30) REVERT: F 62 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.7454 (ttt-90) REVERT: F 66 ARG cc_start: 0.8948 (tpp-160) cc_final: 0.8107 (mmt90) REVERT: G 14 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7765 (mm-30) REVERT: G 20 ASP cc_start: 0.8464 (t70) cc_final: 0.8154 (t0) REVERT: G 21 MET cc_start: 0.8941 (ttp) cc_final: 0.8706 (tmm) REVERT: G 31 ARG cc_start: 0.9139 (ttm-80) cc_final: 0.8845 (ttm-80) REVERT: G 42 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7447 (mm-30) REVERT: H 31 ARG cc_start: 0.8920 (mtm-85) cc_final: 0.8451 (mtm-85) REVERT: I 14 GLU cc_start: 0.8770 (tp30) cc_final: 0.8545 (tp30) REVERT: I 21 MET cc_start: 0.9105 (tmm) cc_final: 0.8194 (tmm) REVERT: I 25 MET cc_start: 0.8711 (ptp) cc_final: 0.8114 (ptp) REVERT: I 43 LEU cc_start: 0.8386 (tp) cc_final: 0.8174 (tp) REVERT: I 64 ARG cc_start: 0.8583 (ptm-80) cc_final: 0.8152 (ptm-80) REVERT: L 69 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7777 (tm-30) REVERT: L 76 GLU cc_start: 0.7958 (pp20) cc_final: 0.7735 (pp20) REVERT: N 20 ASP cc_start: 0.7999 (t0) cc_final: 0.7769 (t0) outliers start: 62 outliers final: 36 residues processed: 472 average time/residue: 0.2684 time to fit residues: 172.7996 Evaluate side-chains 441 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 404 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 161 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 175 ILE 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 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 195 HIS 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 48 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 37 HIS 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: 0.8980 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** E 51 HIS F 61 GLN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS K 13 GLN ** 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: 0.8189 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 12651 Z= 0.353 Angle : 0.779 15.126 17008 Z= 0.401 Chirality : 0.046 0.272 1873 Planarity : 0.004 0.040 2183 Dihedral : 9.394 152.742 1739 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.71 % Allowed : 23.23 % Favored : 71.05 % 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: 0.67 (0.22), residues: 1531 helix: 1.42 (0.16), residues: 1062 sheet: -1.29 (0.54), residues: 87 loop : -1.91 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 244 HIS 0.025 0.002 HIS K 71 PHE 0.021 0.002 PHE A 81 TYR 0.021 0.002 TYR O 38 ARG 0.006 0.001 ARG L 62 *********************** 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 509 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 433 time to evaluate : 1.501 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: 0.7604 (mtpt) cc_final: 0.7238 (mttp) REVERT: A 123 MET cc_start: 0.7876 (ttp) cc_final: 0.7162 (mmt) REVERT: A 140 GLU cc_start: 0.8334 (pp20) cc_final: 0.7549 (tp30) REVERT: B 241 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8428 (mt) REVERT: B 310 THR cc_start: 0.7032 (t) cc_final: 0.6477 (t) REVERT: B 390 TYR cc_start: 0.8568 (m-80) cc_final: 0.8268 (m-10) REVERT: C 135 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8147 (pm20) REVERT: C 218 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8324 (tmtt) REVERT: D 17 PHE cc_start: 0.8933 (t80) cc_final: 0.8668 (t80) REVERT: D 23 LYS cc_start: 0.9478 (ttmt) cc_final: 0.9196 (mttt) REVERT: E 18 LEU cc_start: 0.8729 (mt) cc_final: 0.8401 (pp) REVERT: E 50 GLU cc_start: 0.9354 (tt0) cc_final: 0.9046 (tp30) REVERT: E 55 LYS cc_start: 0.8570 (ptpp) cc_final: 0.8243 (ptpp) REVERT: E 58 LYS cc_start: 0.9122 (mtpt) cc_final: 0.8881 (ptmt) REVERT: E 62 ARG cc_start: 0.8797 (ttt90) cc_final: 0.8484 (ttt90) REVERT: E 66 ARG cc_start: 0.8026 (tpt90) cc_final: 0.7819 (tpt90) REVERT: F 50 GLU cc_start: 0.8163 (pt0) cc_final: 0.7438 (tm-30) REVERT: F 61 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8452 (mm110) REVERT: F 66 ARG cc_start: 0.9011 (tpp-160) cc_final: 0.8101 (mpt-90) REVERT: G 17 MET cc_start: 0.8359 (ppp) cc_final: 0.7456 (ppp) REVERT: G 20 ASP cc_start: 0.8475 (t70) cc_final: 0.8249 (t0) REVERT: G 31 ARG cc_start: 0.9159 (ttm-80) cc_final: 0.8801 (ttm-80) REVERT: G 42 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7620 (mm-30) REVERT: H 31 ARG cc_start: 0.8901 (mtm-85) cc_final: 0.8497 (mtm-85) REVERT: I 14 GLU cc_start: 0.8819 (tp30) cc_final: 0.8587 (tp30) REVERT: I 21 MET cc_start: 0.9106 (tmm) cc_final: 0.8391 (tmm) REVERT: I 25 MET cc_start: 0.8770 (ptp) cc_final: 0.8140 (ptm) REVERT: I 43 LEU cc_start: 0.8510 (tp) cc_final: 0.8285 (tp) REVERT: I 58 TYR cc_start: 0.8844 (t80) cc_final: 0.8560 (t80) REVERT: J 9 GLN cc_start: 0.8633 (tp40) cc_final: 0.8379 (tp40) REVERT: K 40 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: K 58 LYS cc_start: 0.8244 (mmmm) cc_final: 0.8031 (mmmm) REVERT: L 69 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8106 (tm-30) REVERT: L 76 GLU cc_start: 0.8029 (pp20) cc_final: 0.7796 (pp20) outliers start: 76 outliers final: 46 residues processed: 476 average time/residue: 0.2741 time to fit residues: 178.1939 Evaluate side-chains 451 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 402 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 161 ILE 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 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 387 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 HIS 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 46 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 52 ASP 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 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 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 24 LEU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG 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: 0.9990 chunk 131 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 85 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 0.0370 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- 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 57 ASN E 51 HIS ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 61 GLN K 71 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12651 Z= 0.236 Angle : 0.782 12.199 17008 Z= 0.398 Chirality : 0.044 0.246 1873 Planarity : 0.004 0.046 2183 Dihedral : 9.102 153.403 1739 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.44 % Allowed : 25.49 % 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: 0.90 (0.22), residues: 1531 helix: 1.58 (0.16), residues: 1051 sheet: -1.23 (0.53), residues: 89 loop : -1.68 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 244 HIS 0.012 0.001 HIS E 51 PHE 0.027 0.001 PHE A 81 TYR 0.016 0.001 TYR N 22 ARG 0.015 0.001 ARG C 197 *********************** 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 504 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 445 time to evaluate : 1.346 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: A 72 LYS cc_start: 0.7553 (mtpt) cc_final: 0.7187 (mttp) REVERT: A 123 MET cc_start: 0.7905 (ttp) cc_final: 0.7198 (mmt) REVERT: B 107 LYS cc_start: 0.8212 (mttm) cc_final: 0.7747 (ptpp) REVERT: B 163 THR cc_start: 0.8844 (p) cc_final: 0.8642 (t) REVERT: B 241 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8420 (mp) REVERT: B 310 THR cc_start: 0.6851 (t) cc_final: 0.6324 (t) REVERT: B 390 TYR cc_start: 0.8551 (m-80) cc_final: 0.8314 (m-10) REVERT: C 199 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8473 (t) REVERT: C 222 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7241 (pp) REVERT: D 23 LYS cc_start: 0.9462 (ttmt) cc_final: 0.9152 (mttt) REVERT: D 26 GLU cc_start: 0.8513 (tt0) cc_final: 0.8296 (mt-10) REVERT: D 39 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8053 (tpt90) REVERT: E 18 LEU cc_start: 0.8666 (mt) cc_final: 0.8356 (pp) REVERT: E 50 GLU cc_start: 0.9345 (tt0) cc_final: 0.9043 (tp30) REVERT: E 55 LYS cc_start: 0.8559 (ptpp) cc_final: 0.8223 (ptpp) REVERT: E 58 LYS cc_start: 0.9104 (mtpt) cc_final: 0.8897 (ptmt) REVERT: E 62 ARG cc_start: 0.8757 (ttt90) cc_final: 0.8417 (ttt90) REVERT: F 50 GLU cc_start: 0.8150 (pt0) cc_final: 0.7379 (tm-30) REVERT: G 20 ASP cc_start: 0.8280 (t70) cc_final: 0.7942 (t0) REVERT: G 22 TYR cc_start: 0.9065 (t80) cc_final: 0.8718 (t80) REVERT: G 31 ARG cc_start: 0.9127 (ttm-80) cc_final: 0.8829 (ttm-80) REVERT: I 14 GLU cc_start: 0.8823 (tp30) cc_final: 0.8581 (tp30) REVERT: I 21 MET cc_start: 0.9080 (tmm) cc_final: 0.8350 (tmm) REVERT: I 25 MET cc_start: 0.8861 (ptp) cc_final: 0.8025 (ptm) REVERT: I 43 LEU cc_start: 0.8426 (tp) cc_final: 0.8174 (tp) REVERT: I 58 TYR cc_start: 0.8824 (t80) cc_final: 0.8554 (t80) REVERT: J 12 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7509 (ttp80) REVERT: J 27 LEU cc_start: 0.9611 (tp) cc_final: 0.9405 (tt) REVERT: K 12 LYS cc_start: 0.8332 (mmtm) cc_final: 0.7901 (mmtm) REVERT: K 13 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7383 (pt0) REVERT: K 40 GLU cc_start: 0.8259 (pm20) cc_final: 0.7965 (pm20) REVERT: K 58 LYS cc_start: 0.8288 (mmmm) cc_final: 0.7436 (mmmm) REVERT: L 69 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8153 (tm-30) REVERT: L 76 GLU cc_start: 0.8058 (pp20) cc_final: 0.7808 (pp20) outliers start: 59 outliers final: 43 residues processed: 478 average time/residue: 0.2890 time to fit residues: 187.5282 Evaluate side-chains 449 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 402 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 161 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 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 308 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 72 LEU 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 33 CYS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 55 VAL 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 75 VAL Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 24 LEU 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 23 LYS Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 50 CYS 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: 6.9990 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** E 51 HIS ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS K 13 GLN K 54 GLN K 71 HIS K 75 ASN ** M 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 12651 Z= 0.307 Angle : 0.810 12.399 17008 Z= 0.417 Chirality : 0.047 0.308 1873 Planarity : 0.004 0.043 2183 Dihedral : 9.030 151.587 1738 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.71 % Allowed : 25.26 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1531 helix: 1.55 (0.16), residues: 1049 sheet: -1.15 (0.54), residues: 91 loop : -1.58 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 244 HIS 0.013 0.001 HIS E 51 PHE 0.028 0.002 PHE A 81 TYR 0.019 0.001 TYR H 22 ARG 0.008 0.001 ARG H 31 *********************** 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 497 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 421 time to evaluate : 1.481 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 67 GLU cc_start: 0.8102 (pp20) cc_final: 0.7658 (pp20) REVERT: A 72 LYS cc_start: 0.7641 (mtpt) cc_final: 0.7344 (mttp) REVERT: A 123 MET cc_start: 0.7891 (ttp) cc_final: 0.7082 (mmt) REVERT: B 241 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8348 (mt) REVERT: B 390 TYR cc_start: 0.8617 (m-80) cc_final: 0.8402 (m-10) REVERT: C 199 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8752 (t) REVERT: C 222 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7254 (pp) REVERT: D 23 LYS cc_start: 0.9483 (ttmt) cc_final: 0.9168 (mttt) REVERT: D 26 GLU cc_start: 0.8534 (tt0) cc_final: 0.8289 (mt-10) REVERT: D 39 ARG cc_start: 0.8540 (ttp80) cc_final: 0.8027 (tpt90) REVERT: E 18 LEU cc_start: 0.8714 (mt) cc_final: 0.8389 (pp) REVERT: E 50 GLU cc_start: 0.9323 (tt0) cc_final: 0.9045 (tp30) REVERT: E 55 LYS cc_start: 0.8686 (ptpp) cc_final: 0.8454 (ptpp) REVERT: E 58 LYS cc_start: 0.9125 (mtpt) cc_final: 0.8881 (ptmt) REVERT: E 62 ARG cc_start: 0.8776 (ttt90) cc_final: 0.8373 (ttt90) REVERT: G 20 ASP cc_start: 0.8381 (t70) cc_final: 0.8041 (t0) REVERT: G 31 ARG cc_start: 0.9107 (ttm-80) cc_final: 0.8827 (ttm-80) REVERT: I 14 GLU cc_start: 0.8797 (tp30) cc_final: 0.8556 (tp30) REVERT: I 21 MET cc_start: 0.9075 (tmm) cc_final: 0.8366 (tmm) REVERT: I 25 MET cc_start: 0.8936 (ptp) cc_final: 0.8114 (ptm) REVERT: I 43 LEU cc_start: 0.8480 (tp) cc_final: 0.8248 (tp) REVERT: I 58 TYR cc_start: 0.8852 (t80) cc_final: 0.8556 (t80) REVERT: J 9 GLN cc_start: 0.8701 (tp40) cc_final: 0.8485 (tp40) REVERT: K 40 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: L 69 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8154 (tm-30) outliers start: 76 outliers final: 54 residues processed: 461 average time/residue: 0.2695 time to fit residues: 169.0846 Evaluate side-chains 461 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 403 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 161 ILE 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 175 ILE 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 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 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 186 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 71 HIS 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 52 ASP Chi-restraints excluded: chain G residue 72 LEU 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 33 CYS 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 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL 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 7 GLU Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 69 LEU 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: 4.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** C 191 HIS E 51 HIS ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 71 HIS L 68 GLN ** M 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12651 Z= 0.254 Angle : 0.821 12.624 17008 Z= 0.420 Chirality : 0.046 0.296 1873 Planarity : 0.004 0.044 2183 Dihedral : 8.942 150.730 1738 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.04 % Allowed : 26.17 % 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: 0.88 (0.22), residues: 1531 helix: 1.50 (0.16), residues: 1047 sheet: -1.05 (0.53), residues: 93 loop : -1.47 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 244 HIS 0.015 0.001 HIS E 51 PHE 0.028 0.001 PHE A 81 TYR 0.018 0.001 TYR E 21 ARG 0.008 0.001 ARG H 31 *********************** 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 499 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 432 time to evaluate : 1.417 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: A 67 GLU cc_start: 0.8091 (pp20) cc_final: 0.7638 (pp20) REVERT: A 72 LYS cc_start: 0.7680 (mtpt) cc_final: 0.7386 (mttp) REVERT: A 123 MET cc_start: 0.7924 (ttp) cc_final: 0.7131 (mmt) REVERT: A 135 MET cc_start: 0.7928 (ttm) cc_final: 0.7712 (ttt) REVERT: B 107 LYS cc_start: 0.8246 (mttm) cc_final: 0.7632 (ptpp) REVERT: B 241 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8378 (mp) REVERT: C 199 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8761 (t) REVERT: C 216 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8327 (ttpp) REVERT: D 23 LYS cc_start: 0.9485 (ttmt) cc_final: 0.9262 (mttt) REVERT: D 26 GLU cc_start: 0.8569 (tt0) cc_final: 0.8317 (mt-10) REVERT: D 45 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8515 (mp0) REVERT: E 18 LEU cc_start: 0.8683 (mt) cc_final: 0.8373 (pp) REVERT: E 50 GLU cc_start: 0.9311 (tt0) cc_final: 0.9038 (tp30) REVERT: E 55 LYS cc_start: 0.8641 (ptpp) cc_final: 0.8398 (ptpp) REVERT: E 58 LYS cc_start: 0.9142 (mtpt) cc_final: 0.8827 (ptmt) REVERT: E 62 ARG cc_start: 0.8766 (ttt90) cc_final: 0.8426 (ttt90) REVERT: F 61 GLN cc_start: 0.8746 (mm110) cc_final: 0.8487 (mm110) REVERT: G 20 ASP cc_start: 0.8340 (t70) cc_final: 0.8029 (t0) REVERT: G 31 ARG cc_start: 0.9085 (ttm-80) cc_final: 0.8818 (ttm-80) REVERT: H 18 MET cc_start: 0.8613 (mmp) cc_final: 0.8405 (mmm) REVERT: I 14 GLU cc_start: 0.8758 (tp30) cc_final: 0.8535 (tp30) REVERT: I 21 MET cc_start: 0.9075 (tmm) cc_final: 0.8269 (tmm) REVERT: I 25 MET cc_start: 0.8867 (ptp) cc_final: 0.8049 (ptm) REVERT: I 43 LEU cc_start: 0.8546 (tp) cc_final: 0.8314 (tp) REVERT: I 54 CYS cc_start: 0.4577 (m) cc_final: 0.3981 (m) REVERT: I 58 TYR cc_start: 0.8839 (t80) cc_final: 0.8502 (t80) REVERT: J 9 GLN cc_start: 0.8733 (tp40) cc_final: 0.8097 (tp-100) REVERT: K 40 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: L 69 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8157 (tm-30) outliers start: 67 outliers final: 56 residues processed: 464 average time/residue: 0.2837 time to fit residues: 179.4718 Evaluate side-chains 471 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 412 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 36 ASN 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 175 ILE 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 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 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 186 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 72 LEU 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 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL 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 61 GLN Chi-restraints excluded: chain K residue 65 MET 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 59 MET Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 50 CYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG 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: 1.9990 chunk 135 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 71 HIS L 68 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: 0.8149 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12651 Z= 0.270 Angle : 0.871 13.131 17008 Z= 0.437 Chirality : 0.047 0.290 1873 Planarity : 0.004 0.044 2183 Dihedral : 8.906 148.678 1738 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.59 % Allowed : 28.35 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1531 helix: 1.40 (0.16), residues: 1049 sheet: -1.07 (0.55), residues: 91 loop : -1.48 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 244 HIS 0.016 0.001 HIS E 51 PHE 0.029 0.001 PHE A 81 TYR 0.019 0.001 TYR N 22 ARG 0.011 0.001 ARG H 31 *********************** 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 495 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 434 time to evaluate : 1.586 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 72 LYS cc_start: 0.7677 (mtpt) cc_final: 0.7389 (mttp) REVERT: A 123 MET cc_start: 0.7920 (ttp) cc_final: 0.7086 (mmt) REVERT: A 135 MET cc_start: 0.8020 (ttm) cc_final: 0.7808 (ttt) REVERT: B 241 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8366 (mp) REVERT: C 199 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8765 (t) REVERT: C 216 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8371 (ttpp) REVERT: D 23 LYS cc_start: 0.9483 (ttmt) cc_final: 0.9202 (mttt) REVERT: D 26 GLU cc_start: 0.8568 (tt0) cc_final: 0.8332 (mt-10) REVERT: D 39 ARG cc_start: 0.8417 (ttp80) cc_final: 0.7993 (tpt90) REVERT: D 45 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8494 (mp0) REVERT: E 18 LEU cc_start: 0.8680 (mt) cc_final: 0.8365 (pp) REVERT: E 50 GLU cc_start: 0.9345 (tt0) cc_final: 0.9066 (tp30) REVERT: E 55 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8475 (ptpp) REVERT: E 58 LYS cc_start: 0.9073 (mtpt) cc_final: 0.8830 (ptmt) REVERT: F 61 GLN cc_start: 0.8740 (mm110) cc_final: 0.8398 (mm110) REVERT: F 66 ARG cc_start: 0.8822 (tpp-160) cc_final: 0.7965 (mpt-90) REVERT: F 71 HIS cc_start: 0.6447 (m-70) cc_final: 0.6221 (m-70) REVERT: G 14 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7430 (mm-30) REVERT: G 20 ASP cc_start: 0.8371 (t70) cc_final: 0.8033 (t0) REVERT: G 31 ARG cc_start: 0.9048 (ttm-80) cc_final: 0.8824 (ttm-80) REVERT: I 14 GLU cc_start: 0.8724 (tp30) cc_final: 0.8499 (tp30) REVERT: I 21 MET cc_start: 0.9062 (tmm) cc_final: 0.8223 (tmm) REVERT: I 25 MET cc_start: 0.8871 (ptp) cc_final: 0.8038 (ptm) REVERT: I 58 TYR cc_start: 0.8841 (t80) cc_final: 0.8491 (t80) REVERT: J 9 GLN cc_start: 0.8966 (tp40) cc_final: 0.8204 (tp-100) REVERT: J 10 GLN cc_start: 0.8745 (pt0) cc_final: 0.8423 (pp30) REVERT: J 13 ASN cc_start: 0.8255 (m110) cc_final: 0.7747 (m-40) REVERT: J 82 TYR cc_start: 0.5464 (t80) cc_final: 0.4988 (m-10) REVERT: K 40 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: L 69 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8212 (tm-30) outliers start: 61 outliers final: 53 residues processed: 465 average time/residue: 0.2812 time to fit residues: 176.4699 Evaluate side-chains 467 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 410 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 36 ASN 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 175 ILE 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 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 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 186 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 ASP 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 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL 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 61 GLN 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 59 MET Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG 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: 0.7980 chunk 68 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.0570 chunk 127 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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** D 54 GLN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 HIS L 68 GLN M 7 GLN ** 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: 0.8129 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12651 Z= 0.259 Angle : 0.901 14.033 17008 Z= 0.453 Chirality : 0.047 0.267 1873 Planarity : 0.004 0.043 2183 Dihedral : 8.805 147.600 1738 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.44 % Allowed : 28.95 % Favored : 66.62 % 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: 1.43 (0.16), residues: 1050 sheet: -1.12 (0.54), residues: 93 loop : -1.44 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 28 HIS 0.017 0.001 HIS E 51 PHE 0.028 0.001 PHE A 81 TYR 0.022 0.001 TYR H 22 ARG 0.010 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 486 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 427 time to evaluate : 1.507 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: A 72 LYS cc_start: 0.7564 (mtpt) cc_final: 0.7281 (mttp) REVERT: A 123 MET cc_start: 0.7954 (ttp) cc_final: 0.7131 (mmt) REVERT: A 135 MET cc_start: 0.8005 (ttm) cc_final: 0.7783 (ttt) REVERT: B 241 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8290 (mp) REVERT: C 199 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8759 (t) REVERT: C 216 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8454 (ttpp) REVERT: D 23 LYS cc_start: 0.9483 (ttmt) cc_final: 0.9197 (mttt) REVERT: D 26 GLU cc_start: 0.8540 (tt0) cc_final: 0.8299 (mt-10) REVERT: D 39 ARG cc_start: 0.8386 (ttp80) cc_final: 0.8023 (tpt90) REVERT: E 18 LEU cc_start: 0.8684 (mt) cc_final: 0.8349 (pp) REVERT: E 50 GLU cc_start: 0.9359 (tt0) cc_final: 0.9089 (tp30) REVERT: E 55 LYS cc_start: 0.8704 (ptpp) cc_final: 0.8085 (ptpp) REVERT: E 62 ARG cc_start: 0.8697 (ttt90) cc_final: 0.8433 (ttt90) REVERT: F 61 GLN cc_start: 0.8754 (mm110) cc_final: 0.8341 (mm110) REVERT: F 65 MET cc_start: 0.8636 (ptp) cc_final: 0.8302 (ptp) REVERT: F 66 ARG cc_start: 0.8970 (tpp-160) cc_final: 0.7933 (mpt-90) REVERT: G 16 GLU cc_start: 0.8217 (pp20) cc_final: 0.8013 (pp20) REVERT: G 20 ASP cc_start: 0.8319 (t70) cc_final: 0.8008 (t0) REVERT: G 31 ARG cc_start: 0.9021 (ttm-80) cc_final: 0.8806 (ttm-80) REVERT: I 14 GLU cc_start: 0.8755 (tp30) cc_final: 0.8512 (tp30) REVERT: I 21 MET cc_start: 0.9065 (tmm) cc_final: 0.8230 (tmm) REVERT: I 25 MET cc_start: 0.8888 (ptp) cc_final: 0.8106 (ptm) REVERT: J 9 GLN cc_start: 0.8801 (tp40) cc_final: 0.8092 (tp-100) REVERT: J 10 GLN cc_start: 0.8747 (pt0) cc_final: 0.8403 (pp30) REVERT: J 13 ASN cc_start: 0.8305 (m110) cc_final: 0.7804 (m-40) REVERT: J 82 TYR cc_start: 0.5417 (t80) cc_final: 0.4905 (m-10) REVERT: K 40 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8044 (pm20) REVERT: L 69 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8083 (tm-30) outliers start: 59 outliers final: 48 residues processed: 456 average time/residue: 0.2766 time to fit residues: 170.8344 Evaluate side-chains 469 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 418 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 36 ASN 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 175 ILE 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 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 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 186 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain G residue 25 MET 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 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL 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 7 GLU Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 50 CYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG 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: 0.6980 chunk 110 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** E 51 HIS ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 71 HIS L 68 GLN ** O 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3799 r_free = 0.3799 target = 0.116075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.090817 restraints weight = 29417.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089507 restraints weight = 20212.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.090537 restraints weight = 21816.072| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 12651 Z= 0.370 Angle : 0.947 13.890 17008 Z= 0.480 Chirality : 0.050 0.259 1873 Planarity : 0.005 0.041 2183 Dihedral : 8.896 141.216 1738 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.36 % Allowed : 29.70 % Favored : 65.94 % 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: 0.61 (0.22), residues: 1531 helix: 1.24 (0.16), residues: 1057 sheet: -1.32 (0.52), residues: 93 loop : -1.42 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 244 HIS 0.017 0.002 HIS E 51 PHE 0.033 0.002 PHE E 29 TYR 0.022 0.002 TYR N 22 ARG 0.008 0.001 ARG J 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3493.70 seconds wall clock time: 62 minutes 35.65 seconds (3755.65 seconds total)