Starting phenix.real_space_refine on Mon Apr 15 12:45:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5m_21543/04_2024/6w5m_21543.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5m_21543/04_2024/6w5m_21543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5m_21543/04_2024/6w5m_21543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5m_21543/04_2024/6w5m_21543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5m_21543/04_2024/6w5m_21543.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5m_21543/04_2024/6w5m_21543.pdb" } resolution = 4.6 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 Anisotropic ADP refinement not supported. Converting 15451 atoms to isotropic. 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 292 5.49 5 S 58 5.16 5 C 11457 2.51 5 N 3551 2.21 5 O 4216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "C GLU 3891": "OE1" <-> "OE2" Residue "C ARG 3916": "NH1" <-> "NH2" Residue "C ARG 3936": "NH1" <-> "NH2" Residue "C ARG 3965": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D GLU 533": "OE1" <-> "OE2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "M GLU 91": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19574 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2381 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain: "B" Number of atoms: 2302 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 298, 2299 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Conformer: "B" Number of residues, atoms: 298, 2299 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 bond proxies already assigned to first conformer: 2351 Chain: "C" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1185 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1742 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain breaks: 1 Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "P" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 11.60, per 1000 atoms: 0.59 Number of scatterers: 19574 At special positions: 0 Unit cell: (143, 121, 134, 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 58 16.00 P 292 15.00 O 4216 8.00 N 3551 7.00 C 11457 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.33 Conformation dependent library (CDL) restraints added in 2.6 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 27 sheets defined 35.6% alpha, 21.1% beta 156 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 8.59 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'C' and resid 3815 through 3830 removed outlier: 5.141A pdb=" N LYS C3828 " --> pdb=" O LYS C3824 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU C3829 " --> pdb=" O LYS C3825 " (cutoff:3.500A) Processing helix chain 'C' and resid 3867 through 3879 Processing helix chain 'C' and resid 3901 through 3905 removed outlier: 3.523A pdb=" N ILE C3905 " --> pdb=" O ALA C3902 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.804A pdb=" N ARG D 294 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 524 removed outlier: 3.573A pdb=" N MET D 503 " --> pdb=" O PRO D 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 57 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.664A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 removed outlier: 3.586A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.892A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.926A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 26 through 36 Processing helix chain 'I' and resid 45 through 73 removed outlier: 4.524A pdb=" N VAL I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 Processing helix chain 'I' and resid 112 through 116 Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 81 Processing helix chain 'J' and resid 87 through 99 Processing helix chain 'J' and resid 101 through 120 removed outlier: 3.538A pdb=" N LYS J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.664A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 131 removed outlier: 3.585A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.892A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL L 65 " --> pdb=" O PHE L 61 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.924A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 36 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.523A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 88 removed outlier: 3.662A pdb=" N LEU M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 98 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 100 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.936A pdb=" N THR A 29 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 48 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 50 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 74 removed outlier: 3.780A pdb=" N SER A 71 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 90 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG A 103 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLN A 92 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 116 removed outlier: 6.543A pdb=" N CYS A 126 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 113 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 124 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR A 115 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LYS A 122 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 159 removed outlier: 4.504A pdb=" N LYS A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 179 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 185 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.144A pdb=" N GLU A 280 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 286 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 303 removed outlier: 6.528A pdb=" N ILE A 313 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 301 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA A 311 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 42 removed outlier: 5.425A pdb=" N LEU B 37 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS B 331 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 39 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 326 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 53 removed outlier: 3.542A pdb=" N SER B 64 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLY B 73 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE B 79 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 95 removed outlier: 3.890A pdb=" N THR B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP B 115 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS B 121 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 132 through 137 removed outlier: 6.438A pdb=" N VAL B 153 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 166 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 155 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 174 through 179 removed outlier: 3.910A pdb=" N CYS B 195 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASP B 199 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N CYS B 205 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 217 through 222 removed outlier: 3.564A pdb=" N PHE B 219 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 238 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 251 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 240 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 264 through 267 removed outlier: 5.851A pdb=" N VAL B 283 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS B 296 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 285 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 3831 through 3835 Processing sheet with id=AB7, first strand: chain 'C' and resid 3854 through 3857 removed outlier: 7.067A pdb=" N MET C3854 " --> pdb=" O ALA C3930 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA C3930 " --> pdb=" O MET C3854 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3860 through 3864 Processing sheet with id=AB9, first strand: chain 'C' and resid 3906 through 3907 removed outlier: 6.904A pdb=" N ASN C3906 " --> pdb=" O TYR C3942 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 298 through 301 Processing sheet with id=AC2, first strand: chain 'D' and resid 314 through 317 removed outlier: 3.931A pdb=" N THR D 372 " --> pdb=" O ARG D 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 454 through 460 removed outlier: 5.951A pdb=" N PHE D 449 " --> pdb=" O GLN D 456 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL D 458 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE D 447 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR D 479 " --> pdb=" O ASP D 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.363A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.182A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 77 through 78 removed outlier: 3.755A pdb=" N ILE I 78 " --> pdb=" O GLY J 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.405A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.259A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'M' and resid 77 through 78 652 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 396 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 156 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 9.48 Time building geometry restraints manager: 11.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4830 1.33 - 1.45: 5417 1.45 - 1.57: 9654 1.57 - 1.69: 582 1.69 - 1.81: 82 Bond restraints: 20565 Sorted by residual: bond pdb=" C3' DT P 15 " pdb=" O3' DT P 15 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.83e+00 bond pdb=" C3' DC P 126 " pdb=" O3' DC P 126 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" C4' DG P 112 " pdb=" O4' DG P 112 " ideal model delta sigma weight residual 1.450 1.476 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C PRO D 530 " pdb=" N PRO D 531 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.61e+00 bond pdb=" C1' DC O 96 " pdb=" N1 DC O 96 " ideal model delta sigma weight residual 1.490 1.453 0.037 3.00e-02 1.11e+03 1.50e+00 ... (remaining 20560 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.15: 1379 105.15 - 112.40: 11365 112.40 - 119.64: 6437 119.64 - 126.89: 9009 126.89 - 134.14: 882 Bond angle restraints: 29072 Sorted by residual: angle pdb=" N ILE A 66 " pdb=" CA ILE A 66 " pdb=" C ILE A 66 " ideal model delta sigma weight residual 112.35 104.62 7.73 1.41e+00 5.03e-01 3.01e+01 angle pdb=" CA ILE A 66 " pdb=" C ILE A 66 " pdb=" N HIS A 67 " ideal model delta sigma weight residual 117.99 113.91 4.08 1.22e+00 6.72e-01 1.12e+01 angle pdb=" CA TRP D 505 " pdb=" CB TRP D 505 " pdb=" CG TRP D 505 " ideal model delta sigma weight residual 113.60 119.08 -5.48 1.90e+00 2.77e-01 8.31e+00 angle pdb=" N GLY D 485 " pdb=" CA GLY D 485 " pdb=" C GLY D 485 " ideal model delta sigma weight residual 112.34 117.97 -5.63 2.04e+00 2.40e-01 7.61e+00 angle pdb=" C3' DT P 15 " pdb=" O3' DT P 15 " pdb=" P DC P 16 " ideal model delta sigma weight residual 120.20 124.31 -4.11 1.50e+00 4.44e-01 7.50e+00 ... (remaining 29067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 9946 35.18 - 70.37: 1546 70.37 - 105.55: 44 105.55 - 140.74: 3 140.74 - 175.92: 2 Dihedral angle restraints: 11541 sinusoidal: 6537 harmonic: 5004 Sorted by residual: dihedral pdb=" CA PRO D 531 " pdb=" C PRO D 531 " pdb=" N TRP D 532 " pdb=" CA TRP D 532 " ideal model delta harmonic sigma weight residual -180.00 -149.89 -30.11 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA ASN L 64 " pdb=" C ASN L 64 " pdb=" N VAL L 65 " pdb=" CA VAL L 65 " ideal model delta harmonic sigma weight residual -180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ASN H 64 " pdb=" C ASN H 64 " pdb=" N VAL H 65 " pdb=" CA VAL H 65 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 11538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2756 0.057 - 0.115: 475 0.115 - 0.172: 42 0.172 - 0.230: 5 0.230 - 0.287: 1 Chirality restraints: 3279 Sorted by residual: chirality pdb=" CA ILE A 66 " pdb=" N ILE A 66 " pdb=" C ILE A 66 " pdb=" CB ILE A 66 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CG LEU K 100 " pdb=" CB LEU K 100 " pdb=" CD1 LEU K 100 " pdb=" CD2 LEU K 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CG LEU H 58 " pdb=" CB LEU H 58 " pdb=" CD1 LEU H 58 " pdb=" CD2 LEU H 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.55e-01 ... (remaining 3276 not shown) Planarity restraints: 2665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 485 " 0.051 5.00e-02 4.00e+02 7.75e-02 9.61e+00 pdb=" N PRO D 486 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 486 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 486 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 531 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" C PRO D 531 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO D 531 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP D 532 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC O 54 " 0.002 2.00e-02 2.50e+03 1.54e-02 5.30e+00 pdb=" N1 DC O 54 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DC O 54 " 0.039 2.00e-02 2.50e+03 pdb=" O2 DC O 54 " -0.021 2.00e-02 2.50e+03 pdb=" N3 DC O 54 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC O 54 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC O 54 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC O 54 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC O 54 " -0.002 2.00e-02 2.50e+03 ... (remaining 2662 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 216 2.45 - 3.06: 13837 3.06 - 3.67: 38477 3.67 - 4.29: 52484 4.29 - 4.90: 75713 Nonbonded interactions: 180727 Sorted by model distance: nonbonded pdb=" OG1 THR N 29 " pdb=" OP1 DT O 104 " model vdw 1.832 2.440 nonbonded pdb=" O GLU L 74 " pdb=" NH2 ARG N 89 " model vdw 1.961 2.520 nonbonded pdb=" NH1 ARG M 29 " pdb=" O SER N 33 " model vdw 1.996 2.520 nonbonded pdb=" CE LYS G 122 " pdb=" NZ LYS K 115 " model vdw 2.060 3.520 nonbonded pdb=" NH2 ARG I 77 " pdb=" O4' DA O 131 " model vdw 2.070 2.520 ... (remaining 180722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'I' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'M' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'J' selection = (chain 'N' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.010 Extract box with map and model: 6.520 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 65.350 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.005 0.050 20565 Z= 0.305 Angle : 0.682 13.229 29072 Z= 0.400 Chirality : 0.043 0.287 3279 Planarity : 0.005 0.078 2665 Dihedral : 25.405 175.923 8321 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 36.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.58 % Allowed : 6.66 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.98 (0.18), residues: 1699 helix: -1.56 (0.19), residues: 578 sheet: -1.88 (0.24), residues: 373 loop : -2.25 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 505 HIS 0.005 0.001 HIS G 39 PHE 0.019 0.002 PHE D 484 TYR 0.016 0.002 TYR J 118 ARG 0.005 0.001 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 533 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.1024 (t0) cc_final: 0.0773 (m-30) REVERT: A 80 LYS cc_start: 0.1410 (mmtt) cc_final: 0.0948 (mtmt) REVERT: A 137 LEU cc_start: 0.3783 (mt) cc_final: 0.3453 (mm) REVERT: A 213 PHE cc_start: 0.5150 (p90) cc_final: 0.4762 (p90) REVERT: A 247 ASP cc_start: 0.0821 (t0) cc_final: 0.0590 (t0) REVERT: C 3931 MET cc_start: -0.0630 (mtp) cc_final: -0.1048 (ttp) REVERT: D 288 LEU cc_start: 0.6546 (mt) cc_final: 0.6311 (mt) REVERT: D 336 MET cc_start: 0.4982 (tmm) cc_final: 0.3617 (mmt) REVERT: G 58 THR cc_start: 0.8511 (m) cc_final: 0.8163 (p) REVERT: G 65 LEU cc_start: 0.9331 (mt) cc_final: 0.8888 (mm) REVERT: G 73 GLU cc_start: 0.8546 (tt0) cc_final: 0.8219 (tm-30) REVERT: G 74 ILE cc_start: 0.9396 (mm) cc_final: 0.9183 (mm) REVERT: G 97 GLU cc_start: 0.9206 (mt-10) cc_final: 0.7132 (mt-10) REVERT: G 120 MET cc_start: 0.8152 (tpp) cc_final: 0.7944 (tpp) REVERT: H 44 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8046 (mtmt) REVERT: H 67 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8218 (tmm-80) REVERT: I 32 ARG cc_start: 0.8658 (tmm-80) cc_final: 0.8356 (tpt170) REVERT: I 50 TYR cc_start: 0.8824 (t80) cc_final: 0.8065 (t80) REVERT: I 56 GLU cc_start: 0.9256 (tt0) cc_final: 0.8841 (tt0) REVERT: I 65 LEU cc_start: 0.9203 (mt) cc_final: 0.8895 (mt) REVERT: J 38 VAL cc_start: 0.9625 (m) cc_final: 0.9204 (m) REVERT: J 59 MET cc_start: 0.9238 (mmm) cc_final: 0.9027 (mmp) REVERT: J 92 GLN cc_start: 0.8689 (mt0) cc_final: 0.8086 (tp40) REVERT: J 106 HIS cc_start: 0.8611 (m-70) cc_final: 0.8000 (m170) REVERT: K 59 GLU cc_start: 0.8256 (pm20) cc_final: 0.8020 (pm20) REVERT: K 73 GLU cc_start: 0.8644 (tt0) cc_final: 0.8441 (mt-10) REVERT: K 82 LEU cc_start: 0.8648 (mt) cc_final: 0.8448 (mm) REVERT: K 84 PHE cc_start: 0.8293 (m-80) cc_final: 0.7703 (m-80) REVERT: K 94 GLU cc_start: 0.9175 (tp30) cc_final: 0.8922 (tp30) REVERT: K 105 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8862 (tm-30) REVERT: L 51 TYR cc_start: 0.7804 (m-10) cc_final: 0.7372 (m-10) REVERT: L 66 ILE cc_start: 0.9659 (mp) cc_final: 0.9358 (tt) REVERT: M 23 LEU cc_start: 0.8292 (mt) cc_final: 0.7874 (mt) REVERT: M 56 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8174 (mt-10) REVERT: M 57 TYR cc_start: 0.9008 (t80) cc_final: 0.8226 (t80) REVERT: M 61 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8858 (mm-30) REVERT: M 65 LEU cc_start: 0.9414 (mt) cc_final: 0.9112 (mt) REVERT: M 68 ASN cc_start: 0.7909 (m-40) cc_final: 0.7502 (m110) REVERT: M 87 VAL cc_start: 0.8959 (t) cc_final: 0.8498 (t) REVERT: M 88 ARG cc_start: 0.9060 (mmt180) cc_final: 0.8785 (mmp80) REVERT: M 90 ASP cc_start: 0.9080 (t0) cc_final: 0.8847 (t0) REVERT: M 91 GLU cc_start: 0.8622 (pm20) cc_final: 0.8032 (tm-30) REVERT: N 65 ASP cc_start: 0.9012 (t0) cc_final: 0.8649 (t0) REVERT: N 91 ILE cc_start: 0.9062 (mm) cc_final: 0.8721 (mm) REVERT: N 92 GLN cc_start: 0.8888 (tt0) cc_final: 0.8459 (tm-30) REVERT: N 117 LYS cc_start: 0.7177 (tttm) cc_final: 0.6798 (tttp) outliers start: 23 outliers final: 6 residues processed: 537 average time/residue: 0.4077 time to fit residues: 306.6879 Evaluate side-chains 359 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 352 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 58 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN A 285 ASN ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 287 ASN B 289 GLN C3839 HIS ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 76 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 ASN J 60 ASN K 68 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 HIS L 25 ASN M 31 HIS ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN M 104 GLN N 46 HIS ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.189 20565 Z= 0.406 Angle : 0.778 10.305 29072 Z= 0.433 Chirality : 0.047 0.186 3279 Planarity : 0.007 0.063 2665 Dihedral : 29.631 176.434 5081 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.27 % Allowed : 5.56 % Favored : 94.17 % 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: -1.68 (0.19), residues: 1699 helix: -0.09 (0.20), residues: 591 sheet: -1.31 (0.25), residues: 377 loop : -1.79 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 327 HIS 0.009 0.002 HIS J 46 PHE 0.031 0.003 PHE G 67 TYR 0.024 0.003 TYR J 80 ARG 0.035 0.001 ARG M 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 402 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.1530 (t0) cc_final: 0.1260 (m-30) REVERT: A 80 LYS cc_start: 0.1114 (mmtt) cc_final: 0.0746 (mtmt) REVERT: A 119 ASP cc_start: 0.3519 (t0) cc_final: 0.3296 (m-30) REVERT: A 137 LEU cc_start: 0.4181 (mt) cc_final: 0.3893 (mm) REVERT: A 213 PHE cc_start: 0.5174 (p90) cc_final: 0.4728 (p90) REVERT: C 3883 TYR cc_start: 0.4990 (m-80) cc_final: 0.4685 (m-80) REVERT: C 3931 MET cc_start: -0.0331 (mtp) cc_final: -0.0999 (ttt) REVERT: D 336 MET cc_start: 0.4326 (tmm) cc_final: 0.3710 (mmt) REVERT: G 51 ILE cc_start: 0.9422 (mt) cc_final: 0.9218 (mt) REVERT: G 55 GLN cc_start: 0.8760 (mt0) cc_final: 0.8188 (mt0) REVERT: G 97 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8443 (mt-10) REVERT: G 105 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8886 (tm-30) REVERT: G 119 ILE cc_start: 0.8651 (pt) cc_final: 0.8005 (pt) REVERT: H 27 GLN cc_start: 0.8975 (pp30) cc_final: 0.8532 (pp30) REVERT: H 54 THR cc_start: 0.9652 (m) cc_final: 0.9263 (p) REVERT: H 64 ASN cc_start: 0.9218 (m-40) cc_final: 0.8887 (m-40) REVERT: H 65 VAL cc_start: 0.9785 (m) cc_final: 0.9509 (m) REVERT: H 67 ARG cc_start: 0.9349 (ttp-110) cc_final: 0.8731 (ttp80) REVERT: H 68 ASP cc_start: 0.9256 (m-30) cc_final: 0.8730 (p0) REVERT: H 75 HIS cc_start: 0.8762 (t-90) cc_final: 0.8226 (t-90) REVERT: H 84 MET cc_start: 0.9200 (mmm) cc_final: 0.8893 (mmm) REVERT: H 88 TYR cc_start: 0.8987 (m-10) cc_final: 0.8583 (m-10) REVERT: I 25 PHE cc_start: 0.9126 (m-10) cc_final: 0.8824 (m-10) REVERT: I 32 ARG cc_start: 0.9006 (tmm-80) cc_final: 0.8642 (tmm-80) REVERT: I 38 ASN cc_start: 0.9502 (m110) cc_final: 0.9252 (m-40) REVERT: I 42 ARG cc_start: 0.8793 (mtm180) cc_final: 0.8519 (mtm-85) REVERT: I 64 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8540 (tm-30) REVERT: I 84 GLN cc_start: 0.9532 (tp40) cc_final: 0.9306 (tp-100) REVERT: I 90 ASP cc_start: 0.9018 (t0) cc_final: 0.8652 (t0) REVERT: I 92 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8547 (mt-10) REVERT: I 99 ARG cc_start: 0.9079 (ptp90) cc_final: 0.8420 (ttm110) REVERT: J 59 MET cc_start: 0.9254 (mmm) cc_final: 0.8999 (mmm) REVERT: J 103 LEU cc_start: 0.9630 (mt) cc_final: 0.9358 (mt) REVERT: J 106 HIS cc_start: 0.8494 (m-70) cc_final: 0.7989 (m170) REVERT: K 59 GLU cc_start: 0.8584 (pm20) cc_final: 0.8381 (pm20) REVERT: K 61 LEU cc_start: 0.8798 (mm) cc_final: 0.8445 (mm) REVERT: K 73 GLU cc_start: 0.8293 (tt0) cc_final: 0.7818 (tt0) REVERT: K 77 ASP cc_start: 0.9404 (t0) cc_final: 0.9172 (t70) REVERT: K 80 THR cc_start: 0.8507 (p) cc_final: 0.7873 (p) REVERT: K 81 ASP cc_start: 0.8510 (m-30) cc_final: 0.8171 (m-30) REVERT: K 84 PHE cc_start: 0.8423 (m-80) cc_final: 0.7925 (m-80) REVERT: K 85 GLN cc_start: 0.8905 (mp-120) cc_final: 0.8565 (mm110) REVERT: K 90 MET cc_start: 0.9310 (mmm) cc_final: 0.9068 (mmm) REVERT: K 93 GLN cc_start: 0.8750 (pp30) cc_final: 0.7948 (tm-30) REVERT: K 94 GLU cc_start: 0.9179 (tp30) cc_final: 0.8879 (tp30) REVERT: K 97 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8107 (mm-30) REVERT: K 120 MET cc_start: 0.9008 (tpp) cc_final: 0.8512 (mmm) REVERT: L 25 ASN cc_start: 0.8411 (m110) cc_final: 0.8172 (m110) REVERT: L 37 LEU cc_start: 0.9454 (mt) cc_final: 0.9168 (mt) REVERT: L 45 ARG cc_start: 0.9178 (tpp80) cc_final: 0.8005 (tpp80) REVERT: L 53 GLU cc_start: 0.9002 (tp30) cc_final: 0.8658 (tp30) REVERT: L 63 GLU cc_start: 0.9006 (tp30) cc_final: 0.8441 (tm-30) REVERT: L 66 ILE cc_start: 0.9675 (OUTLIER) cc_final: 0.9376 (tt) REVERT: L 93 GLN cc_start: 0.9374 (tp40) cc_final: 0.8883 (tp40) REVERT: M 57 TYR cc_start: 0.8958 (t80) cc_final: 0.8039 (t80) REVERT: M 61 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8782 (mm-30) REVERT: M 68 ASN cc_start: 0.7809 (m-40) cc_final: 0.7545 (m110) REVERT: M 87 VAL cc_start: 0.9036 (t) cc_final: 0.8742 (t) REVERT: M 100 VAL cc_start: 0.9393 (t) cc_final: 0.9127 (t) REVERT: M 108 LEU cc_start: 0.9442 (pt) cc_final: 0.9097 (pt) REVERT: N 30 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7289 (mtt180) REVERT: N 59 MET cc_start: 0.9342 (mmp) cc_final: 0.9103 (mmp) REVERT: N 68 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8429 (mm-30) REVERT: N 81 ASN cc_start: 0.8910 (t0) cc_final: 0.8497 (t0) REVERT: N 92 GLN cc_start: 0.9260 (tt0) cc_final: 0.8654 (tm-30) outliers start: 4 outliers final: 1 residues processed: 404 average time/residue: 0.3545 time to fit residues: 209.8166 Evaluate side-chains 333 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 331 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN G 76 GLN G 93 GLN ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS K 68 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 64 ASN ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN N 106 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 20565 Z= 0.295 Angle : 0.667 9.684 29072 Z= 0.374 Chirality : 0.042 0.250 3279 Planarity : 0.005 0.063 2665 Dihedral : 29.584 177.552 5081 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.14 % Allowed : 3.36 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.02 (0.20), residues: 1699 helix: 0.63 (0.20), residues: 601 sheet: -1.20 (0.26), residues: 371 loop : -1.44 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 505 HIS 0.009 0.001 HIS H 75 PHE 0.019 0.002 PHE G 67 TYR 0.020 0.002 TYR K 54 ARG 0.005 0.001 ARG H 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 399 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.2074 (t0) cc_final: 0.1751 (m-30) REVERT: A 80 LYS cc_start: 0.0892 (mmtt) cc_final: 0.0502 (mtmt) REVERT: A 137 LEU cc_start: 0.4296 (mt) cc_final: 0.4046 (mm) REVERT: A 213 PHE cc_start: 0.5061 (p90) cc_final: 0.4385 (p90) REVERT: B 288 LEU cc_start: 0.6257 (tp) cc_final: 0.6026 (pt) REVERT: C 3883 TYR cc_start: 0.4885 (m-80) cc_final: 0.4562 (m-80) REVERT: C 3931 MET cc_start: -0.0660 (mtp) cc_final: -0.1182 (ttt) REVERT: D 336 MET cc_start: 0.4290 (tmm) cc_final: 0.3771 (mmt) REVERT: G 55 GLN cc_start: 0.8726 (mt0) cc_final: 0.8524 (mt0) REVERT: G 65 LEU cc_start: 0.9382 (mm) cc_final: 0.9055 (mm) REVERT: G 104 PHE cc_start: 0.9512 (m-80) cc_final: 0.9275 (m-80) REVERT: G 119 ILE cc_start: 0.8332 (pt) cc_final: 0.7745 (pt) REVERT: G 120 MET cc_start: 0.8366 (mmt) cc_final: 0.7764 (mmm) REVERT: H 27 GLN cc_start: 0.8958 (pp30) cc_final: 0.8683 (pp30) REVERT: H 51 TYR cc_start: 0.8613 (m-80) cc_final: 0.8242 (m-80) REVERT: H 63 GLU cc_start: 0.9124 (tp30) cc_final: 0.8783 (tp30) REVERT: H 65 VAL cc_start: 0.9772 (m) cc_final: 0.9341 (p) REVERT: H 67 ARG cc_start: 0.9291 (ttp-110) cc_final: 0.8959 (ttm110) REVERT: H 68 ASP cc_start: 0.9217 (m-30) cc_final: 0.8750 (p0) REVERT: H 74 GLU cc_start: 0.8440 (tp30) cc_final: 0.8079 (tp30) REVERT: H 75 HIS cc_start: 0.8739 (t-90) cc_final: 0.8396 (t-90) REVERT: H 88 TYR cc_start: 0.9012 (m-10) cc_final: 0.8683 (m-10) REVERT: I 25 PHE cc_start: 0.9066 (m-10) cc_final: 0.8832 (m-10) REVERT: I 32 ARG cc_start: 0.8959 (tmm-80) cc_final: 0.8565 (tpt170) REVERT: I 38 ASN cc_start: 0.9487 (m110) cc_final: 0.9191 (m-40) REVERT: I 64 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8568 (tm-30) REVERT: I 90 ASP cc_start: 0.8975 (t0) cc_final: 0.8599 (t0) REVERT: I 92 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8651 (mt-10) REVERT: I 99 ARG cc_start: 0.8984 (ptp90) cc_final: 0.8293 (ttm110) REVERT: I 104 GLN cc_start: 0.8649 (mp10) cc_final: 0.7990 (mp10) REVERT: J 99 LEU cc_start: 0.8599 (mp) cc_final: 0.8390 (mp) REVERT: J 106 HIS cc_start: 0.8249 (m90) cc_final: 0.7694 (m170) REVERT: K 73 GLU cc_start: 0.8279 (tt0) cc_final: 0.7593 (tt0) REVERT: K 80 THR cc_start: 0.8391 (p) cc_final: 0.7638 (p) REVERT: K 81 ASP cc_start: 0.8342 (m-30) cc_final: 0.8078 (m-30) REVERT: K 93 GLN cc_start: 0.8497 (pp30) cc_final: 0.8288 (pp30) REVERT: K 94 GLU cc_start: 0.9106 (tp30) cc_final: 0.8853 (tp30) REVERT: K 97 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8759 (mt-10) REVERT: K 105 GLU cc_start: 0.9295 (tt0) cc_final: 0.8953 (tm-30) REVERT: L 22 LEU cc_start: 0.8123 (mm) cc_final: 0.7846 (mm) REVERT: L 25 ASN cc_start: 0.8478 (m110) cc_final: 0.7639 (m110) REVERT: L 45 ARG cc_start: 0.9264 (tpp80) cc_final: 0.8919 (tpp80) REVERT: L 62 LEU cc_start: 0.9723 (mp) cc_final: 0.9478 (mp) REVERT: L 67 ARG cc_start: 0.8877 (ttp80) cc_final: 0.8203 (ttp80) REVERT: L 85 ASP cc_start: 0.9103 (m-30) cc_final: 0.8803 (m-30) REVERT: L 88 TYR cc_start: 0.8465 (m-80) cc_final: 0.6909 (m-10) REVERT: L 98 TYR cc_start: 0.8252 (m-80) cc_final: 0.8044 (m-80) REVERT: M 57 TYR cc_start: 0.9253 (t80) cc_final: 0.8459 (t80) REVERT: M 61 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8629 (mm-30) REVERT: M 64 GLU cc_start: 0.8962 (pp20) cc_final: 0.8480 (pp20) REVERT: M 65 LEU cc_start: 0.9536 (mt) cc_final: 0.9246 (mt) REVERT: M 72 ASP cc_start: 0.8426 (m-30) cc_final: 0.7833 (t70) REVERT: M 84 GLN cc_start: 0.9266 (tp-100) cc_final: 0.8880 (tp-100) REVERT: M 87 VAL cc_start: 0.9302 (t) cc_final: 0.9085 (p) REVERT: M 90 ASP cc_start: 0.9270 (t0) cc_final: 0.9053 (t0) REVERT: M 95 LYS cc_start: 0.8894 (ttmt) cc_final: 0.8624 (ttmt) REVERT: M 108 LEU cc_start: 0.9514 (pt) cc_final: 0.9250 (pt) REVERT: N 38 VAL cc_start: 0.9834 (t) cc_final: 0.9468 (t) REVERT: N 65 ASP cc_start: 0.9047 (t70) cc_final: 0.8765 (t0) REVERT: N 81 ASN cc_start: 0.9200 (t0) cc_final: 0.8746 (t0) REVERT: N 92 GLN cc_start: 0.9249 (tt0) cc_final: 0.8749 (tm-30) outliers start: 2 outliers final: 0 residues processed: 400 average time/residue: 0.3465 time to fit residues: 202.8254 Evaluate side-chains 332 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN G 76 GLN J 46 HIS K 68 GLN L 93 GLN ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.169 20565 Z= 0.384 Angle : 0.727 12.158 29072 Z= 0.404 Chirality : 0.044 0.166 3279 Planarity : 0.005 0.056 2665 Dihedral : 29.639 177.955 5081 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 25.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.23 % 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: -1.04 (0.19), residues: 1699 helix: 0.41 (0.20), residues: 592 sheet: -0.94 (0.26), residues: 357 loop : -1.39 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 505 HIS 0.009 0.002 HIS H 75 PHE 0.031 0.002 PHE G 67 TYR 0.027 0.002 TYR H 98 ARG 0.004 0.001 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 371 time to evaluate : 1.722 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: A 80 LYS cc_start: 0.0789 (mmtt) cc_final: 0.0340 (mtmt) REVERT: A 213 PHE cc_start: 0.5031 (p90) cc_final: 0.4426 (p90) REVERT: B 314 ASN cc_start: 0.5763 (m-40) cc_final: 0.5560 (m-40) REVERT: C 3883 TYR cc_start: 0.4780 (m-80) cc_final: 0.4424 (m-80) REVERT: D 336 MET cc_start: 0.4292 (tmm) cc_final: 0.3751 (mmt) REVERT: G 55 GLN cc_start: 0.8721 (mt0) cc_final: 0.8329 (mt0) REVERT: G 65 LEU cc_start: 0.9460 (mm) cc_final: 0.9222 (mm) REVERT: G 105 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8895 (tm-30) REVERT: G 119 ILE cc_start: 0.8337 (pt) cc_final: 0.7495 (pt) REVERT: G 120 MET cc_start: 0.8492 (mmt) cc_final: 0.7669 (mmm) REVERT: H 27 GLN cc_start: 0.9005 (pp30) cc_final: 0.8726 (pp30) REVERT: H 44 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8606 (mmmm) REVERT: H 63 GLU cc_start: 0.9240 (tp30) cc_final: 0.8793 (tp30) REVERT: H 65 VAL cc_start: 0.9745 (m) cc_final: 0.9414 (p) REVERT: H 67 ARG cc_start: 0.9416 (ttp-110) cc_final: 0.8893 (ttm110) REVERT: H 68 ASP cc_start: 0.9381 (m-30) cc_final: 0.8884 (p0) REVERT: H 73 THR cc_start: 0.9732 (m) cc_final: 0.9506 (p) REVERT: H 74 GLU cc_start: 0.8459 (tp30) cc_final: 0.7977 (tp30) REVERT: H 88 TYR cc_start: 0.9024 (m-10) cc_final: 0.8704 (m-10) REVERT: H 92 ARG cc_start: 0.8747 (tmm160) cc_final: 0.8138 (tmm160) REVERT: I 25 PHE cc_start: 0.9070 (m-10) cc_final: 0.8780 (m-10) REVERT: I 32 ARG cc_start: 0.9044 (tmm-80) cc_final: 0.8635 (tpt170) REVERT: I 38 ASN cc_start: 0.9505 (m110) cc_final: 0.9148 (m110) REVERT: I 64 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8668 (tm-30) REVERT: I 90 ASP cc_start: 0.8987 (t0) cc_final: 0.8651 (t70) REVERT: I 92 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8580 (mt-10) REVERT: I 104 GLN cc_start: 0.8751 (mp10) cc_final: 0.8174 (mp10) REVERT: J 92 GLN cc_start: 0.9516 (tt0) cc_final: 0.8540 (tp40) REVERT: J 103 LEU cc_start: 0.9630 (mt) cc_final: 0.9180 (mt) REVERT: J 105 LYS cc_start: 0.8448 (mttt) cc_final: 0.7960 (ptmt) REVERT: K 48 LEU cc_start: 0.9407 (mt) cc_final: 0.9080 (mt) REVERT: K 60 LEU cc_start: 0.8419 (mt) cc_final: 0.8139 (mt) REVERT: K 73 GLU cc_start: 0.8180 (tt0) cc_final: 0.7566 (tt0) REVERT: K 77 ASP cc_start: 0.9389 (t70) cc_final: 0.9127 (t0) REVERT: K 80 THR cc_start: 0.8290 (p) cc_final: 0.7465 (p) REVERT: K 81 ASP cc_start: 0.8438 (m-30) cc_final: 0.8117 (m-30) REVERT: K 93 GLN cc_start: 0.8759 (pp30) cc_final: 0.8391 (pp30) REVERT: K 94 GLU cc_start: 0.9282 (tp30) cc_final: 0.9005 (tp30) REVERT: K 97 GLU cc_start: 0.9216 (mt-10) cc_final: 0.7933 (mm-30) REVERT: K 105 GLU cc_start: 0.9398 (tt0) cc_final: 0.9024 (pp20) REVERT: K 120 MET cc_start: 0.8579 (mmt) cc_final: 0.8172 (mmt) REVERT: L 22 LEU cc_start: 0.8166 (mm) cc_final: 0.7850 (mm) REVERT: L 25 ASN cc_start: 0.8532 (m110) cc_final: 0.7639 (m110) REVERT: L 31 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8993 (ttmt) REVERT: L 37 LEU cc_start: 0.9544 (mt) cc_final: 0.9119 (mt) REVERT: L 45 ARG cc_start: 0.9184 (tpp80) cc_final: 0.8512 (tpp80) REVERT: L 82 THR cc_start: 0.8807 (p) cc_final: 0.8488 (p) REVERT: L 84 MET cc_start: 0.8956 (mpp) cc_final: 0.8645 (mpp) REVERT: L 88 TYR cc_start: 0.8910 (m-80) cc_final: 0.8473 (m-80) REVERT: L 93 GLN cc_start: 0.9436 (tp40) cc_final: 0.9041 (tp40) REVERT: M 41 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8347 (mp0) REVERT: M 54 VAL cc_start: 0.9591 (t) cc_final: 0.9369 (t) REVERT: M 55 LEU cc_start: 0.9817 (mt) cc_final: 0.9614 (mt) REVERT: M 57 TYR cc_start: 0.9428 (t80) cc_final: 0.8595 (t80) REVERT: M 61 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8869 (mm-30) REVERT: M 64 GLU cc_start: 0.9106 (pp20) cc_final: 0.8816 (pp20) REVERT: M 68 ASN cc_start: 0.8513 (m110) cc_final: 0.7976 (m110) REVERT: M 108 LEU cc_start: 0.9551 (pt) cc_final: 0.9236 (pt) REVERT: M 115 LEU cc_start: 0.8669 (mt) cc_final: 0.8389 (mt) REVERT: N 56 MET cc_start: 0.9284 (tpp) cc_final: 0.9070 (tpp) REVERT: N 81 ASN cc_start: 0.9250 (t0) cc_final: 0.8800 (t0) REVERT: N 92 GLN cc_start: 0.9338 (tt0) cc_final: 0.8633 (tm-30) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 0.3354 time to fit residues: 184.8713 Evaluate side-chains 317 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 139 optimal weight: 0.0040 chunk 77 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 95 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN G 76 GLN H 25 ASN J 60 ASN J 106 HIS K 68 GLN L 27 GLN M 24 GLN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20565 Z= 0.213 Angle : 0.640 8.477 29072 Z= 0.358 Chirality : 0.042 0.167 3279 Planarity : 0.005 0.061 2665 Dihedral : 29.406 178.717 5081 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % 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: -0.66 (0.20), residues: 1699 helix: 0.81 (0.20), residues: 605 sheet: -0.90 (0.27), residues: 352 loop : -1.19 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 505 HIS 0.008 0.001 HIS H 75 PHE 0.020 0.002 PHE G 67 TYR 0.022 0.002 TYR G 54 ARG 0.010 0.001 ARG L 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 1.838 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: A 61 ILE cc_start: 0.1253 (mm) cc_final: 0.0758 (pt) REVERT: A 80 LYS cc_start: 0.0992 (mmtt) cc_final: 0.0526 (mtmt) REVERT: A 213 PHE cc_start: 0.5048 (p90) cc_final: 0.4593 (p90) REVERT: A 279 TRP cc_start: 0.1314 (m-90) cc_final: 0.0806 (m-90) REVERT: B 314 ASN cc_start: 0.5616 (m-40) cc_final: 0.5413 (m-40) REVERT: C 3883 TYR cc_start: 0.4503 (m-80) cc_final: 0.4129 (m-80) REVERT: C 3931 MET cc_start: -0.0874 (mtt) cc_final: -0.1517 (ttm) REVERT: D 327 TRP cc_start: 0.7645 (p-90) cc_final: 0.7413 (p-90) REVERT: D 336 MET cc_start: 0.4958 (tmm) cc_final: 0.4068 (mmt) REVERT: D 518 TYR cc_start: -0.2502 (t80) cc_final: -0.3120 (m-80) REVERT: G 42 ARG cc_start: 0.8144 (mmp80) cc_final: 0.7806 (mmp80) REVERT: G 50 GLU cc_start: 0.9369 (tp30) cc_final: 0.9041 (tp30) REVERT: G 51 ILE cc_start: 0.9371 (mt) cc_final: 0.9123 (mt) REVERT: G 55 GLN cc_start: 0.8768 (mt0) cc_final: 0.8218 (mt0) REVERT: G 58 THR cc_start: 0.9496 (p) cc_final: 0.9254 (p) REVERT: G 65 LEU cc_start: 0.9433 (mm) cc_final: 0.9101 (mm) REVERT: G 84 PHE cc_start: 0.9437 (m-80) cc_final: 0.9128 (m-10) REVERT: G 93 GLN cc_start: 0.8333 (pp30) cc_final: 0.8033 (pp30) REVERT: G 119 ILE cc_start: 0.8424 (pt) cc_final: 0.7911 (pt) REVERT: G 120 MET cc_start: 0.8499 (mmt) cc_final: 0.7930 (mmm) REVERT: G 124 ILE cc_start: 0.9399 (pt) cc_final: 0.9172 (pt) REVERT: H 63 GLU cc_start: 0.9159 (tp30) cc_final: 0.8619 (tp30) REVERT: H 65 VAL cc_start: 0.9705 (m) cc_final: 0.9414 (p) REVERT: H 67 ARG cc_start: 0.9263 (ttp-110) cc_final: 0.8849 (ttm110) REVERT: H 68 ASP cc_start: 0.9199 (m-30) cc_final: 0.8776 (p0) REVERT: H 73 THR cc_start: 0.9740 (m) cc_final: 0.9443 (p) REVERT: H 74 GLU cc_start: 0.8235 (tp30) cc_final: 0.7609 (tp30) REVERT: H 80 THR cc_start: 0.9323 (p) cc_final: 0.9083 (p) REVERT: I 32 ARG cc_start: 0.8905 (tmm-80) cc_final: 0.8623 (tpt170) REVERT: I 38 ASN cc_start: 0.9424 (m110) cc_final: 0.9121 (m110) REVERT: I 61 GLU cc_start: 0.8736 (mp0) cc_final: 0.8405 (mp0) REVERT: I 64 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8565 (tm-30) REVERT: I 84 GLN cc_start: 0.9301 (tp-100) cc_final: 0.8993 (tp-100) REVERT: I 92 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8074 (mt-10) REVERT: I 104 GLN cc_start: 0.8649 (mp10) cc_final: 0.8131 (mp10) REVERT: J 103 LEU cc_start: 0.9380 (mt) cc_final: 0.9137 (mt) REVERT: J 105 LYS cc_start: 0.8321 (mttt) cc_final: 0.7928 (ptmt) REVERT: K 60 LEU cc_start: 0.8161 (mt) cc_final: 0.7876 (mt) REVERT: K 73 GLU cc_start: 0.8193 (tt0) cc_final: 0.7542 (tt0) REVERT: K 77 ASP cc_start: 0.9370 (t70) cc_final: 0.9151 (t0) REVERT: K 84 PHE cc_start: 0.8484 (m-80) cc_final: 0.8251 (m-80) REVERT: K 85 GLN cc_start: 0.8982 (mm110) cc_final: 0.8781 (mm110) REVERT: K 93 GLN cc_start: 0.8730 (pp30) cc_final: 0.8517 (pp30) REVERT: K 105 GLU cc_start: 0.9341 (tt0) cc_final: 0.8934 (pp20) REVERT: K 120 MET cc_start: 0.8425 (mmt) cc_final: 0.8043 (mmt) REVERT: L 22 LEU cc_start: 0.8214 (mm) cc_final: 0.7883 (mm) REVERT: L 25 ASN cc_start: 0.8484 (m110) cc_final: 0.7566 (m110) REVERT: L 37 LEU cc_start: 0.9434 (mt) cc_final: 0.8966 (mt) REVERT: L 45 ARG cc_start: 0.9201 (tpp80) cc_final: 0.8754 (tpp80) REVERT: L 67 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8363 (ttp80) REVERT: L 75 HIS cc_start: 0.9429 (t-90) cc_final: 0.8866 (t-170) REVERT: L 82 THR cc_start: 0.9112 (p) cc_final: 0.8397 (p) REVERT: L 85 ASP cc_start: 0.9340 (m-30) cc_final: 0.9068 (m-30) REVERT: L 88 TYR cc_start: 0.8720 (m-80) cc_final: 0.8241 (m-80) REVERT: L 98 TYR cc_start: 0.8125 (m-80) cc_final: 0.7409 (m-80) REVERT: M 57 TYR cc_start: 0.9319 (t80) cc_final: 0.8304 (t80) REVERT: M 64 GLU cc_start: 0.9080 (pp20) cc_final: 0.8605 (pp20) REVERT: M 65 LEU cc_start: 0.9491 (mt) cc_final: 0.9264 (mt) REVERT: M 68 ASN cc_start: 0.8582 (m110) cc_final: 0.8341 (m110) REVERT: M 72 ASP cc_start: 0.8467 (m-30) cc_final: 0.7970 (t70) REVERT: M 104 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8296 (tp40) REVERT: M 108 LEU cc_start: 0.9550 (pt) cc_final: 0.9135 (pt) REVERT: N 56 MET cc_start: 0.9241 (tpp) cc_final: 0.8957 (tpp) REVERT: N 69 ARG cc_start: 0.9342 (ttm170) cc_final: 0.9002 (ttm110) REVERT: N 81 ASN cc_start: 0.9247 (t0) cc_final: 0.8775 (t0) REVERT: N 92 GLN cc_start: 0.9335 (tt0) cc_final: 0.8736 (tm-30) REVERT: N 110 GLU cc_start: 0.8796 (tt0) cc_final: 0.8558 (tm-30) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.3573 time to fit residues: 212.8362 Evaluate side-chains 327 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 37 optimal weight: 30.0000 chunk 110 optimal weight: 0.9980 chunk 46 optimal weight: 30.0000 chunk 187 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN G 76 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 20565 Z= 0.290 Angle : 0.669 10.296 29072 Z= 0.375 Chirality : 0.043 0.266 3279 Planarity : 0.005 0.062 2665 Dihedral : 29.344 178.665 5081 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: -0.72 (0.20), residues: 1699 helix: 0.69 (0.21), residues: 602 sheet: -0.94 (0.27), residues: 371 loop : -1.13 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 505 HIS 0.020 0.001 HIS D 375 PHE 0.032 0.002 PHE D 488 TYR 0.021 0.002 TYR A 277 ARG 0.006 0.001 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 1.553 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: A 61 ILE cc_start: 0.1391 (mm) cc_final: 0.0854 (pt) REVERT: A 213 PHE cc_start: 0.5122 (p90) cc_final: 0.4636 (p90) REVERT: B 314 ASN cc_start: 0.5985 (m-40) cc_final: 0.5758 (m-40) REVERT: D 327 TRP cc_start: 0.7596 (p-90) cc_final: 0.7364 (p-90) REVERT: D 336 MET cc_start: 0.5056 (tmm) cc_final: 0.4133 (mmt) REVERT: D 518 TYR cc_start: -0.2527 (t80) cc_final: -0.3169 (m-80) REVERT: G 42 ARG cc_start: 0.8162 (mmp80) cc_final: 0.7819 (mmp80) REVERT: G 51 ILE cc_start: 0.9402 (mt) cc_final: 0.9158 (mt) REVERT: G 55 GLN cc_start: 0.8691 (mt0) cc_final: 0.8283 (mt0) REVERT: G 58 THR cc_start: 0.9515 (p) cc_final: 0.9212 (p) REVERT: G 65 LEU cc_start: 0.9480 (mm) cc_final: 0.9121 (mm) REVERT: G 119 ILE cc_start: 0.8371 (pt) cc_final: 0.7764 (pt) REVERT: G 120 MET cc_start: 0.8514 (mmt) cc_final: 0.7936 (mmm) REVERT: G 133 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7790 (mp0) REVERT: H 63 GLU cc_start: 0.9228 (tp30) cc_final: 0.8747 (tp30) REVERT: H 67 ARG cc_start: 0.9255 (ttp-110) cc_final: 0.8813 (ttm110) REVERT: H 73 THR cc_start: 0.9707 (m) cc_final: 0.9489 (p) REVERT: H 74 GLU cc_start: 0.8379 (tp30) cc_final: 0.7607 (tp30) REVERT: H 97 LEU cc_start: 0.9146 (tp) cc_final: 0.8942 (tp) REVERT: I 38 ASN cc_start: 0.9386 (m110) cc_final: 0.9128 (m110) REVERT: I 61 GLU cc_start: 0.8809 (mp0) cc_final: 0.8264 (mp0) REVERT: I 64 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8640 (tm-30) REVERT: I 79 ILE cc_start: 0.9548 (tp) cc_final: 0.9211 (tp) REVERT: I 84 GLN cc_start: 0.9276 (tp-100) cc_final: 0.8974 (tp-100) REVERT: I 90 ASP cc_start: 0.8872 (t0) cc_final: 0.8533 (t70) REVERT: I 92 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8379 (mt-10) REVERT: I 104 GLN cc_start: 0.8606 (mp10) cc_final: 0.8154 (mp10) REVERT: J 81 ASN cc_start: 0.9320 (t0) cc_final: 0.9048 (t0) REVERT: J 92 GLN cc_start: 0.9407 (tt0) cc_final: 0.8369 (tp40) REVERT: J 103 LEU cc_start: 0.9387 (mt) cc_final: 0.9125 (mt) REVERT: J 105 LYS cc_start: 0.8398 (mttt) cc_final: 0.7886 (ptmt) REVERT: K 51 ILE cc_start: 0.9241 (pt) cc_final: 0.8723 (pt) REVERT: K 55 GLN cc_start: 0.8887 (mt0) cc_final: 0.8502 (tt0) REVERT: K 73 GLU cc_start: 0.8228 (tt0) cc_final: 0.7607 (tt0) REVERT: K 77 ASP cc_start: 0.9396 (t70) cc_final: 0.9188 (t0) REVERT: K 93 GLN cc_start: 0.8520 (pp30) cc_final: 0.7967 (pp30) REVERT: K 105 GLU cc_start: 0.9414 (tt0) cc_final: 0.8971 (pp20) REVERT: K 110 CYS cc_start: 0.9036 (t) cc_final: 0.8618 (t) REVERT: K 123 ASP cc_start: 0.7885 (t70) cc_final: 0.6874 (t70) REVERT: L 22 LEU cc_start: 0.8136 (mm) cc_final: 0.7886 (mm) REVERT: L 25 ASN cc_start: 0.8447 (m110) cc_final: 0.7571 (m110) REVERT: L 45 ARG cc_start: 0.9239 (tpp80) cc_final: 0.8887 (tpp80) REVERT: L 67 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8253 (ttp80) REVERT: L 88 TYR cc_start: 0.8625 (m-80) cc_final: 0.8357 (m-80) REVERT: M 56 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9152 (mt-10) REVERT: M 57 TYR cc_start: 0.9341 (t80) cc_final: 0.8761 (t80) REVERT: M 64 GLU cc_start: 0.9144 (pp20) cc_final: 0.8626 (pp20) REVERT: M 65 LEU cc_start: 0.9515 (mt) cc_final: 0.9262 (mt) REVERT: M 68 ASN cc_start: 0.8560 (m110) cc_final: 0.8359 (m110) REVERT: M 72 ASP cc_start: 0.8523 (m-30) cc_final: 0.8042 (t70) REVERT: M 108 LEU cc_start: 0.9578 (pt) cc_final: 0.9257 (pt) REVERT: N 56 MET cc_start: 0.9228 (tpp) cc_final: 0.8959 (tpp) REVERT: N 69 ARG cc_start: 0.9360 (ttm170) cc_final: 0.9023 (ttm110) REVERT: N 81 ASN cc_start: 0.9316 (t0) cc_final: 0.8806 (t0) REVERT: N 92 GLN cc_start: 0.9348 (tt0) cc_final: 0.8688 (tm-30) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.3315 time to fit residues: 185.6816 Evaluate side-chains 305 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN L 27 GLN L 93 GLN N 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20565 Z= 0.216 Angle : 0.644 9.058 29072 Z= 0.360 Chirality : 0.042 0.163 3279 Planarity : 0.005 0.092 2665 Dihedral : 29.251 178.973 5081 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.07 % Allowed : 1.44 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.20), residues: 1699 helix: 0.83 (0.21), residues: 603 sheet: -0.92 (0.27), residues: 363 loop : -1.11 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 505 HIS 0.009 0.001 HIS D 375 PHE 0.016 0.002 PHE I 25 TYR 0.024 0.002 TYR J 37 ARG 0.007 0.000 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 371 time to evaluate : 1.861 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: A 61 ILE cc_start: 0.1225 (mm) cc_final: 0.0738 (pt) REVERT: A 213 PHE cc_start: 0.5008 (p90) cc_final: 0.4553 (p90) REVERT: B 314 ASN cc_start: 0.5936 (m-40) cc_final: 0.5714 (m-40) REVERT: D 327 TRP cc_start: 0.7623 (p-90) cc_final: 0.7285 (p-90) REVERT: D 336 MET cc_start: 0.5309 (tmm) cc_final: 0.4043 (mmt) REVERT: D 518 TYR cc_start: -0.2509 (t80) cc_final: -0.3053 (m-80) REVERT: G 42 ARG cc_start: 0.8101 (mmp80) cc_final: 0.7758 (mmp80) REVERT: G 55 GLN cc_start: 0.8739 (mt0) cc_final: 0.8232 (mt0) REVERT: G 65 LEU cc_start: 0.9409 (mm) cc_final: 0.9054 (mm) REVERT: G 119 ILE cc_start: 0.8500 (pt) cc_final: 0.7915 (pt) REVERT: G 120 MET cc_start: 0.8454 (mmt) cc_final: 0.7893 (mmm) REVERT: H 44 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8525 (mmmt) REVERT: H 63 GLU cc_start: 0.9153 (tp30) cc_final: 0.8599 (tp30) REVERT: H 67 ARG cc_start: 0.9130 (ttp-110) cc_final: 0.8691 (ttm110) REVERT: H 73 THR cc_start: 0.9701 (m) cc_final: 0.9479 (p) REVERT: H 97 LEU cc_start: 0.9163 (tp) cc_final: 0.8882 (tp) REVERT: I 17 ARG cc_start: 0.9323 (mtm180) cc_final: 0.8614 (mtp85) REVERT: I 38 ASN cc_start: 0.9351 (m110) cc_final: 0.9064 (m-40) REVERT: I 57 TYR cc_start: 0.7736 (t80) cc_final: 0.7399 (t80) REVERT: I 64 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8525 (tm-30) REVERT: I 84 GLN cc_start: 0.9238 (tp-100) cc_final: 0.8884 (tp-100) REVERT: I 92 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8159 (mt-10) REVERT: I 104 GLN cc_start: 0.8605 (mp10) cc_final: 0.8132 (mp10) REVERT: J 36 ILE cc_start: 0.9541 (pt) cc_final: 0.9311 (tp) REVERT: J 105 LYS cc_start: 0.8387 (mttt) cc_final: 0.7865 (ptmt) REVERT: K 51 ILE cc_start: 0.9010 (pt) cc_final: 0.8760 (pt) REVERT: K 55 GLN cc_start: 0.8817 (mt0) cc_final: 0.8383 (tt0) REVERT: K 64 LYS cc_start: 0.8713 (mmtp) cc_final: 0.8490 (mmmm) REVERT: K 73 GLU cc_start: 0.8261 (tt0) cc_final: 0.7636 (tt0) REVERT: K 77 ASP cc_start: 0.9406 (t70) cc_final: 0.9174 (t0) REVERT: K 84 PHE cc_start: 0.8796 (m-80) cc_final: 0.8531 (m-80) REVERT: K 93 GLN cc_start: 0.8580 (pp30) cc_final: 0.8327 (pp30) REVERT: K 105 GLU cc_start: 0.9399 (tt0) cc_final: 0.9009 (pp20) REVERT: K 110 CYS cc_start: 0.9084 (t) cc_final: 0.8653 (t) REVERT: K 120 MET cc_start: 0.8404 (mmt) cc_final: 0.8135 (mmt) REVERT: K 123 ASP cc_start: 0.7683 (t70) cc_final: 0.6843 (t70) REVERT: L 25 ASN cc_start: 0.8431 (m110) cc_final: 0.7611 (m110) REVERT: L 45 ARG cc_start: 0.9149 (tpp80) cc_final: 0.8773 (tpp80) REVERT: L 67 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8402 (ttp80) REVERT: L 75 HIS cc_start: 0.9345 (t-90) cc_final: 0.8805 (t-170) REVERT: L 98 TYR cc_start: 0.7933 (m-80) cc_final: 0.7467 (m-80) REVERT: M 43 VAL cc_start: 0.8655 (m) cc_final: 0.8441 (p) REVERT: M 57 TYR cc_start: 0.9353 (t80) cc_final: 0.8572 (t80) REVERT: M 64 GLU cc_start: 0.9118 (pp20) cc_final: 0.8664 (pp20) REVERT: M 65 LEU cc_start: 0.9516 (mt) cc_final: 0.9291 (mt) REVERT: M 68 ASN cc_start: 0.8597 (m110) cc_final: 0.8365 (m110) REVERT: M 72 ASP cc_start: 0.8465 (m-30) cc_final: 0.7948 (t70) REVERT: M 87 VAL cc_start: 0.9308 (t) cc_final: 0.9024 (t) REVERT: M 108 LEU cc_start: 0.9561 (pt) cc_final: 0.9175 (pt) REVERT: N 39 TYR cc_start: 0.7373 (t80) cc_final: 0.6588 (t80) REVERT: N 56 MET cc_start: 0.9220 (tpp) cc_final: 0.8906 (tpp) REVERT: N 65 ASP cc_start: 0.9070 (t70) cc_final: 0.8855 (t0) REVERT: N 69 ARG cc_start: 0.9315 (ttm170) cc_final: 0.9010 (ttm110) REVERT: N 81 ASN cc_start: 0.9296 (t0) cc_final: 0.8786 (t0) REVERT: N 92 GLN cc_start: 0.9352 (tt0) cc_final: 0.8901 (tm-30) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 0.3143 time to fit residues: 177.7550 Evaluate side-chains 312 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 17 optimal weight: 0.4980 chunk 146 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN N 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 20565 Z= 0.245 Angle : 0.645 8.361 29072 Z= 0.361 Chirality : 0.042 0.219 3279 Planarity : 0.005 0.079 2665 Dihedral : 29.156 178.920 5081 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -0.49 (0.20), residues: 1699 helix: 1.00 (0.21), residues: 599 sheet: -0.80 (0.27), residues: 366 loop : -1.12 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 505 HIS 0.009 0.001 HIS H 75 PHE 0.019 0.002 PHE A 189 TYR 0.022 0.002 TYR A 167 ARG 0.006 0.000 ARG I 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 1.747 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 61 ILE cc_start: 0.1207 (mm) cc_final: 0.0722 (pt) REVERT: A 213 PHE cc_start: 0.5119 (p90) cc_final: 0.4569 (p90) REVERT: B 314 ASN cc_start: 0.6100 (m-40) cc_final: 0.5865 (m-40) REVERT: D 327 TRP cc_start: 0.7529 (p-90) cc_final: 0.7285 (p-90) REVERT: D 336 MET cc_start: 0.5406 (tmm) cc_final: 0.4187 (mmt) REVERT: D 518 TYR cc_start: -0.2244 (t80) cc_final: -0.3018 (m-80) REVERT: G 42 ARG cc_start: 0.8089 (mmp80) cc_final: 0.7743 (mmp80) REVERT: G 84 PHE cc_start: 0.9593 (m-80) cc_final: 0.9393 (m-10) REVERT: G 104 PHE cc_start: 0.9393 (m-80) cc_final: 0.9170 (m-80) REVERT: G 119 ILE cc_start: 0.8475 (pt) cc_final: 0.7777 (pt) REVERT: G 120 MET cc_start: 0.8491 (mmt) cc_final: 0.7885 (mmm) REVERT: G 133 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7816 (mp0) REVERT: H 63 GLU cc_start: 0.9153 (tp30) cc_final: 0.8622 (tp30) REVERT: H 67 ARG cc_start: 0.9054 (ttp-110) cc_final: 0.8663 (ttm110) REVERT: H 68 ASP cc_start: 0.9307 (m-30) cc_final: 0.8808 (p0) REVERT: H 97 LEU cc_start: 0.9055 (tp) cc_final: 0.8832 (tp) REVERT: I 38 ASN cc_start: 0.9336 (m110) cc_final: 0.9061 (m-40) REVERT: I 64 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8534 (tm-30) REVERT: I 92 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8312 (mt-10) REVERT: I 104 GLN cc_start: 0.8576 (mp10) cc_final: 0.8119 (mp10) REVERT: J 36 ILE cc_start: 0.9530 (pt) cc_final: 0.9320 (tp) REVERT: J 81 ASN cc_start: 0.9329 (t0) cc_final: 0.8957 (t0) REVERT: J 105 LYS cc_start: 0.8395 (mttt) cc_final: 0.7857 (ptmt) REVERT: K 50 GLU cc_start: 0.8419 (pp20) cc_final: 0.8164 (pp20) REVERT: K 51 ILE cc_start: 0.8990 (pt) cc_final: 0.8725 (pt) REVERT: K 55 GLN cc_start: 0.8783 (mt0) cc_final: 0.8313 (tt0) REVERT: K 73 GLU cc_start: 0.8252 (tt0) cc_final: 0.7669 (tt0) REVERT: K 77 ASP cc_start: 0.9418 (t70) cc_final: 0.9191 (t0) REVERT: K 84 PHE cc_start: 0.8863 (m-80) cc_final: 0.8373 (m-80) REVERT: K 93 GLN cc_start: 0.8511 (pp30) cc_final: 0.8227 (pp30) REVERT: K 105 GLU cc_start: 0.9415 (tt0) cc_final: 0.9019 (pp20) REVERT: K 110 CYS cc_start: 0.9080 (t) cc_final: 0.8646 (t) REVERT: K 120 MET cc_start: 0.8373 (mmt) cc_final: 0.8097 (mmt) REVERT: K 123 ASP cc_start: 0.7777 (t70) cc_final: 0.6890 (t70) REVERT: L 25 ASN cc_start: 0.8437 (m110) cc_final: 0.7721 (m110) REVERT: L 67 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8244 (ttp80) REVERT: L 88 TYR cc_start: 0.8578 (m-80) cc_final: 0.8343 (m-80) REVERT: M 43 VAL cc_start: 0.8744 (m) cc_final: 0.8527 (p) REVERT: M 57 TYR cc_start: 0.9389 (t80) cc_final: 0.8374 (t80) REVERT: M 64 GLU cc_start: 0.9117 (pp20) cc_final: 0.8716 (pp20) REVERT: M 65 LEU cc_start: 0.9484 (mt) cc_final: 0.9219 (mt) REVERT: M 68 ASN cc_start: 0.8581 (m110) cc_final: 0.8365 (m110) REVERT: M 72 ASP cc_start: 0.8447 (m-30) cc_final: 0.7963 (t70) REVERT: M 94 ASN cc_start: 0.9275 (t0) cc_final: 0.9070 (t0) REVERT: M 108 LEU cc_start: 0.9567 (pt) cc_final: 0.9246 (pt) REVERT: N 39 TYR cc_start: 0.7398 (t80) cc_final: 0.6717 (t80) REVERT: N 56 MET cc_start: 0.9212 (tpp) cc_final: 0.8888 (tpp) REVERT: N 65 ASP cc_start: 0.9024 (t70) cc_final: 0.8610 (t0) REVERT: N 69 ARG cc_start: 0.9295 (ttm170) cc_final: 0.8827 (ttm110) REVERT: N 81 ASN cc_start: 0.9311 (t0) cc_final: 0.8765 (t0) REVERT: N 92 GLN cc_start: 0.9333 (tt0) cc_final: 0.8872 (tm-30) REVERT: N 110 GLU cc_start: 0.8767 (tt0) cc_final: 0.8539 (tm-30) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.3034 time to fit residues: 171.3606 Evaluate side-chains 302 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN L 27 GLN M 104 GLN N 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20565 Z= 0.192 Angle : 0.639 11.690 29072 Z= 0.355 Chirality : 0.042 0.204 3279 Planarity : 0.005 0.085 2665 Dihedral : 29.021 179.537 5081 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.07 % Allowed : 0.62 % Favored : 99.31 % 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: -0.49 (0.20), residues: 1699 helix: 1.01 (0.21), residues: 587 sheet: -0.77 (0.27), residues: 371 loop : -1.12 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 505 HIS 0.008 0.001 HIS H 75 PHE 0.020 0.001 PHE K 67 TYR 0.016 0.002 TYR A 167 ARG 0.011 0.001 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 363 time to evaluate : 1.774 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: A 61 ILE cc_start: 0.1113 (mm) cc_final: 0.0626 (pt) REVERT: A 213 PHE cc_start: 0.4987 (p90) cc_final: 0.4550 (p90) REVERT: B 314 ASN cc_start: 0.6050 (m-40) cc_final: 0.5813 (m-40) REVERT: D 327 TRP cc_start: 0.7340 (p-90) cc_final: 0.7138 (p-90) REVERT: D 336 MET cc_start: 0.5220 (tmm) cc_final: 0.4248 (mmt) REVERT: D 518 TYR cc_start: -0.2304 (t80) cc_final: -0.3113 (m-10) REVERT: G 42 ARG cc_start: 0.8104 (mmp80) cc_final: 0.7759 (mmp80) REVERT: G 51 ILE cc_start: 0.9266 (mt) cc_final: 0.8902 (mt) REVERT: G 55 GLN cc_start: 0.8944 (mt0) cc_final: 0.8438 (tt0) REVERT: G 58 THR cc_start: 0.9411 (p) cc_final: 0.9184 (p) REVERT: G 119 ILE cc_start: 0.8460 (pt) cc_final: 0.7896 (pt) REVERT: G 120 MET cc_start: 0.8394 (mmt) cc_final: 0.7854 (mmm) REVERT: H 39 ARG cc_start: 0.9409 (mmt180) cc_final: 0.9071 (mmt180) REVERT: H 44 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8455 (mmmt) REVERT: H 63 GLU cc_start: 0.9091 (tp30) cc_final: 0.8532 (tp30) REVERT: H 67 ARG cc_start: 0.8934 (ttp-110) cc_final: 0.8506 (ttm110) REVERT: H 68 ASP cc_start: 0.9007 (m-30) cc_final: 0.8663 (p0) REVERT: H 97 LEU cc_start: 0.9024 (tp) cc_final: 0.8821 (tp) REVERT: I 25 PHE cc_start: 0.8914 (m-80) cc_final: 0.8633 (m-80) REVERT: I 38 ASN cc_start: 0.9288 (m110) cc_final: 0.8949 (m-40) REVERT: I 57 TYR cc_start: 0.7847 (t80) cc_final: 0.7010 (t80) REVERT: I 61 GLU cc_start: 0.8929 (mp0) cc_final: 0.8290 (mp0) REVERT: I 64 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8510 (tm-30) REVERT: I 92 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8615 (mt-10) REVERT: I 104 GLN cc_start: 0.8708 (mp10) cc_final: 0.8185 (mp10) REVERT: I 107 VAL cc_start: 0.8402 (t) cc_final: 0.8054 (t) REVERT: J 81 ASN cc_start: 0.9335 (t0) cc_final: 0.8944 (t0) REVERT: J 105 LYS cc_start: 0.8342 (mttt) cc_final: 0.7825 (ptmt) REVERT: K 51 ILE cc_start: 0.8927 (pt) cc_final: 0.8607 (pt) REVERT: K 55 GLN cc_start: 0.8616 (mt0) cc_final: 0.8276 (tt0) REVERT: K 73 GLU cc_start: 0.8314 (tt0) cc_final: 0.7721 (tt0) REVERT: K 77 ASP cc_start: 0.9417 (t70) cc_final: 0.9203 (t0) REVERT: K 84 PHE cc_start: 0.8888 (m-80) cc_final: 0.8461 (m-80) REVERT: K 105 GLU cc_start: 0.9412 (tt0) cc_final: 0.9183 (tt0) REVERT: K 107 THR cc_start: 0.9581 (p) cc_final: 0.9361 (p) REVERT: K 120 MET cc_start: 0.8380 (mmt) cc_final: 0.8113 (mmt) REVERT: K 123 ASP cc_start: 0.7667 (t0) cc_final: 0.7254 (t70) REVERT: L 25 ASN cc_start: 0.8310 (m110) cc_final: 0.7629 (m110) REVERT: L 88 TYR cc_start: 0.8652 (m-80) cc_final: 0.8409 (m-80) REVERT: L 93 GLN cc_start: 0.9419 (tp40) cc_final: 0.8882 (tp40) REVERT: M 43 VAL cc_start: 0.8740 (m) cc_final: 0.8454 (p) REVERT: M 57 TYR cc_start: 0.9294 (t80) cc_final: 0.8971 (t80) REVERT: M 64 GLU cc_start: 0.9114 (pp20) cc_final: 0.8656 (pp20) REVERT: M 65 LEU cc_start: 0.9501 (mt) cc_final: 0.9177 (mt) REVERT: M 68 ASN cc_start: 0.8589 (m110) cc_final: 0.8153 (m110) REVERT: M 90 ASP cc_start: 0.8684 (t0) cc_final: 0.8241 (p0) REVERT: M 91 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7775 (tm-30) REVERT: M 94 ASN cc_start: 0.9168 (t0) cc_final: 0.8962 (t0) REVERT: N 39 TYR cc_start: 0.7203 (t80) cc_final: 0.6659 (t80) REVERT: N 56 MET cc_start: 0.9203 (tpp) cc_final: 0.8870 (tpp) REVERT: N 81 ASN cc_start: 0.9356 (t0) cc_final: 0.8795 (t0) REVERT: N 92 GLN cc_start: 0.9350 (tt0) cc_final: 0.8758 (tm-30) outliers start: 1 outliers final: 0 residues processed: 363 average time/residue: 0.2901 time to fit residues: 165.0980 Evaluate side-chains 317 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 118 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS K 68 GLN ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN M 89 ASN M 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20565 Z= 0.196 Angle : 0.632 11.606 29072 Z= 0.353 Chirality : 0.041 0.211 3279 Planarity : 0.005 0.065 2665 Dihedral : 28.902 179.623 5081 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1699 helix: 1.13 (0.21), residues: 587 sheet: -0.72 (0.27), residues: 366 loop : -1.09 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 505 HIS 0.008 0.001 HIS H 75 PHE 0.017 0.001 PHE G 67 TYR 0.016 0.001 TYR J 37 ARG 0.011 0.001 ARG H 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 1.713 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 61 ILE cc_start: 0.1227 (mm) cc_final: 0.0753 (pt) REVERT: A 172 LYS cc_start: 0.4519 (mppt) cc_final: 0.4173 (ptmt) REVERT: A 213 PHE cc_start: 0.5011 (p90) cc_final: 0.4559 (p90) REVERT: B 314 ASN cc_start: 0.6086 (m-40) cc_final: 0.5846 (m-40) REVERT: D 327 TRP cc_start: 0.7461 (p-90) cc_final: 0.7235 (p-90) REVERT: D 336 MET cc_start: 0.5263 (tmm) cc_final: 0.4185 (mmt) REVERT: D 518 TYR cc_start: -0.2246 (t80) cc_final: -0.3086 (m-10) REVERT: G 42 ARG cc_start: 0.8098 (mmp80) cc_final: 0.7725 (mmp80) REVERT: G 58 THR cc_start: 0.9362 (p) cc_final: 0.9075 (p) REVERT: G 65 LEU cc_start: 0.9421 (mm) cc_final: 0.8955 (mm) REVERT: G 104 PHE cc_start: 0.9406 (m-80) cc_final: 0.9183 (m-80) REVERT: G 119 ILE cc_start: 0.8476 (pt) cc_final: 0.7917 (pt) REVERT: G 120 MET cc_start: 0.8368 (mmt) cc_final: 0.7829 (mmm) REVERT: H 39 ARG cc_start: 0.9425 (mmt180) cc_final: 0.9159 (mmt180) REVERT: H 44 LYS cc_start: 0.9259 (mmmt) cc_final: 0.8942 (mmmt) REVERT: H 63 GLU cc_start: 0.9087 (tp30) cc_final: 0.8571 (tp30) REVERT: H 67 ARG cc_start: 0.8913 (ttp-110) cc_final: 0.8640 (ttm110) REVERT: H 68 ASP cc_start: 0.8889 (m-30) cc_final: 0.8673 (p0) REVERT: H 97 LEU cc_start: 0.9047 (tp) cc_final: 0.8810 (tp) REVERT: I 38 ASN cc_start: 0.9259 (m110) cc_final: 0.8925 (m-40) REVERT: I 57 TYR cc_start: 0.7741 (t80) cc_final: 0.6886 (t80) REVERT: I 61 GLU cc_start: 0.8916 (mp0) cc_final: 0.8297 (mp0) REVERT: I 64 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8466 (tm-30) REVERT: I 79 ILE cc_start: 0.9473 (tt) cc_final: 0.9256 (tp) REVERT: I 92 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8263 (mt-10) REVERT: I 104 GLN cc_start: 0.8545 (mp10) cc_final: 0.8118 (mp10) REVERT: I 107 VAL cc_start: 0.8347 (t) cc_final: 0.7980 (t) REVERT: J 79 HIS cc_start: 0.8322 (t-90) cc_final: 0.8094 (t-90) REVERT: J 81 ASN cc_start: 0.9359 (t0) cc_final: 0.8972 (t0) REVERT: J 103 LEU cc_start: 0.9301 (mt) cc_final: 0.9083 (mt) REVERT: J 105 LYS cc_start: 0.8351 (mttt) cc_final: 0.7837 (ptmt) REVERT: K 51 ILE cc_start: 0.9394 (pt) cc_final: 0.9160 (pt) REVERT: K 55 GLN cc_start: 0.8737 (mt0) cc_final: 0.8329 (tt0) REVERT: K 73 GLU cc_start: 0.8321 (tt0) cc_final: 0.7737 (tt0) REVERT: K 77 ASP cc_start: 0.9415 (t70) cc_final: 0.9208 (t0) REVERT: K 84 PHE cc_start: 0.8932 (m-80) cc_final: 0.8531 (m-80) REVERT: K 93 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8109 (tm-30) REVERT: K 105 GLU cc_start: 0.9393 (tt0) cc_final: 0.9158 (tt0) REVERT: K 107 THR cc_start: 0.9621 (p) cc_final: 0.8785 (p) REVERT: K 120 MET cc_start: 0.8421 (mmt) cc_final: 0.8166 (mmt) REVERT: K 123 ASP cc_start: 0.7722 (t0) cc_final: 0.5757 (t70) REVERT: L 25 ASN cc_start: 0.8281 (m110) cc_final: 0.7564 (m110) REVERT: L 88 TYR cc_start: 0.8629 (m-80) cc_final: 0.8305 (m-80) REVERT: L 98 TYR cc_start: 0.7928 (m-80) cc_final: 0.7598 (m-80) REVERT: M 43 VAL cc_start: 0.8699 (m) cc_final: 0.8388 (p) REVERT: M 57 TYR cc_start: 0.9121 (t80) cc_final: 0.8306 (t80) REVERT: M 64 GLU cc_start: 0.9123 (pp20) cc_final: 0.8699 (pp20) REVERT: M 65 LEU cc_start: 0.9491 (mt) cc_final: 0.9219 (mt) REVERT: M 68 ASN cc_start: 0.8587 (m110) cc_final: 0.8133 (m110) REVERT: M 94 ASN cc_start: 0.9188 (t0) cc_final: 0.8978 (t0) REVERT: N 39 TYR cc_start: 0.7143 (t80) cc_final: 0.6584 (t80) REVERT: N 56 MET cc_start: 0.9245 (tpp) cc_final: 0.8895 (tpp) REVERT: N 59 MET cc_start: 0.9429 (mmp) cc_final: 0.9199 (mmp) REVERT: N 65 ASP cc_start: 0.8943 (t70) cc_final: 0.8568 (t0) REVERT: N 69 ARG cc_start: 0.9409 (ttm170) cc_final: 0.8963 (ttm110) REVERT: N 81 ASN cc_start: 0.9337 (t0) cc_final: 0.8794 (t0) REVERT: N 92 GLN cc_start: 0.9345 (tt0) cc_final: 0.8770 (tm-30) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2962 time to fit residues: 167.4560 Evaluate side-chains 313 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 141 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 19 optimal weight: 40.0000 chunk 28 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN L 27 GLN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN N 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.112930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.072898 restraints weight = 87779.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.075106 restraints weight = 43424.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076429 restraints weight = 27328.749| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 20565 Z= 0.255 Angle : 0.648 11.524 29072 Z= 0.362 Chirality : 0.042 0.199 3279 Planarity : 0.005 0.065 2665 Dihedral : 28.929 178.791 5081 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1699 helix: 0.99 (0.21), residues: 585 sheet: -0.69 (0.27), residues: 368 loop : -1.09 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 505 HIS 0.008 0.001 HIS H 75 PHE 0.023 0.002 PHE I 25 TYR 0.019 0.002 TYR J 37 ARG 0.011 0.001 ARG H 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4315.25 seconds wall clock time: 79 minutes 43.16 seconds (4783.16 seconds total)