Starting phenix.real_space_refine on Mon Mar 11 02:54:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teq_41195/03_2024/8teq_41195.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teq_41195/03_2024/8teq_41195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teq_41195/03_2024/8teq_41195.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teq_41195/03_2024/8teq_41195.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teq_41195/03_2024/8teq_41195.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teq_41195/03_2024/8teq_41195.pdb" } resolution = 2.84 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 4185 2.51 5 N 1155 2.21 5 O 1365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6705 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "B" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "C" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "D" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "E" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "F" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "G" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "H" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "I" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "J" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "K" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "L" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "M" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "N" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "O" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "P" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "Q" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "R" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "S" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "T" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "U" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "V" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "W" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "X" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "Y" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "Z" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "0" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "1" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "2" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "3" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Time building chain proxies: 3.55, per 1000 atoms: 0.53 Number of scatterers: 6705 At special positions: 0 Unit cell: (65.36, 65.36, 89.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1365 8.00 N 1155 7.00 C 4185 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: 2.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1530 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing sheet with id=AA1, first strand: chain '0' and resid 266 through 274 removed outlier: 6.765A pdb=" N GLN W 266 " --> pdb=" O GLN 0 267 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL 0 269 " --> pdb=" O GLN W 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR W 268 " --> pdb=" O VAL 0 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN 0 271 " --> pdb=" O TYR W 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE W 270 " --> pdb=" O GLN 0 271 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER 0 273 " --> pdb=" O ILE W 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR W 272 " --> pdb=" O SER 0 273 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN S 266 " --> pdb=" O GLN W 267 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL W 269 " --> pdb=" O GLN S 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR S 268 " --> pdb=" O VAL W 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN W 271 " --> pdb=" O TYR S 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE S 270 " --> pdb=" O GLN W 271 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER W 273 " --> pdb=" O ILE S 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR S 272 " --> pdb=" O SER W 273 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN O 266 " --> pdb=" O GLN S 267 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL S 269 " --> pdb=" O GLN O 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR O 268 " --> pdb=" O VAL S 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN S 271 " --> pdb=" O TYR O 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE O 270 " --> pdb=" O GLN S 271 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER S 273 " --> pdb=" O ILE O 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR O 272 " --> pdb=" O SER S 273 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN K 266 " --> pdb=" O GLN O 267 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL O 269 " --> pdb=" O GLN K 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR K 268 " --> pdb=" O VAL O 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN O 271 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE K 270 " --> pdb=" O GLN O 271 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N SER O 273 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR K 272 " --> pdb=" O SER O 273 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN G 266 " --> pdb=" O GLN K 267 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL K 269 " --> pdb=" O GLN G 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR G 268 " --> pdb=" O VAL K 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN K 271 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE G 270 " --> pdb=" O GLN K 271 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER K 273 " --> pdb=" O ILE G 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR G 272 " --> pdb=" O SER K 273 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN C 266 " --> pdb=" O GLN G 267 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL G 269 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR C 268 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN G 271 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE C 270 " --> pdb=" O GLN G 271 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER G 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR C 272 " --> pdb=" O SER G 273 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN A 266 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL C 269 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR A 268 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN C 271 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 270 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N SER C 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR A 272 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 278 through 279 removed outlier: 6.832A pdb=" N GLN W 278 " --> pdb=" O GLN 0 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN S 278 " --> pdb=" O GLN W 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN O 278 " --> pdb=" O GLN S 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN K 278 " --> pdb=" O GLN O 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN G 278 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN C 278 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN A 278 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 286 through 289 removed outlier: 6.544A pdb=" N GLN A 287 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN E 287 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN I 287 " --> pdb=" O PHE M 288 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN M 287 " --> pdb=" O PHE Q 288 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN Q 287 " --> pdb=" O PHE U 288 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN U 287 " --> pdb=" O PHE Y 288 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN Y 287 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 266 through 273 removed outlier: 6.401A pdb=" N GLN X 267 " --> pdb=" O TYR 1 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE 1 270 " --> pdb=" O GLN X 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL X 269 " --> pdb=" O ILE 1 270 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR 1 272 " --> pdb=" O VAL X 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN X 271 " --> pdb=" O TYR 1 272 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN T 267 " --> pdb=" O TYR X 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE X 270 " --> pdb=" O GLN T 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL T 269 " --> pdb=" O ILE X 270 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR X 272 " --> pdb=" O VAL T 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN T 271 " --> pdb=" O TYR X 272 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN P 267 " --> pdb=" O TYR T 268 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE T 270 " --> pdb=" O GLN P 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL P 269 " --> pdb=" O ILE T 270 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR T 272 " --> pdb=" O VAL P 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN P 271 " --> pdb=" O TYR T 272 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN L 267 " --> pdb=" O TYR P 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE P 270 " --> pdb=" O GLN L 267 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL L 269 " --> pdb=" O ILE P 270 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR P 272 " --> pdb=" O VAL L 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN L 271 " --> pdb=" O TYR P 272 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN H 267 " --> pdb=" O TYR L 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE L 270 " --> pdb=" O GLN H 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL H 269 " --> pdb=" O ILE L 270 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR L 272 " --> pdb=" O VAL H 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN H 271 " --> pdb=" O TYR L 272 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN D 267 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE H 270 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL D 269 " --> pdb=" O ILE H 270 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR H 272 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN D 271 " --> pdb=" O TYR H 272 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN B 267 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE D 270 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 269 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR D 272 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN B 271 " --> pdb=" O TYR D 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 278 through 279 removed outlier: 6.653A pdb=" N GLN B 278 " --> pdb=" O GLN F 279 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN F 278 " --> pdb=" O GLN J 279 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN J 278 " --> pdb=" O GLN N 279 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN N 278 " --> pdb=" O GLN R 279 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN R 278 " --> pdb=" O GLN V 279 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN V 278 " --> pdb=" O GLN Z 279 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN Z 278 " --> pdb=" O GLN 3 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 286 through 289 removed outlier: 6.508A pdb=" N GLN X 287 " --> pdb=" O PHE 1 288 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN T 287 " --> pdb=" O PHE X 288 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN P 287 " --> pdb=" O PHE T 288 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN L 287 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN H 287 " --> pdb=" O PHE L 288 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN D 287 " --> pdb=" O PHE H 288 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN B 287 " --> pdb=" O PHE D 288 " (cutoff:3.500A) 161 hydrogen bonds defined for protein. 483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1155 1.29 - 1.35: 1125 1.35 - 1.41: 813 1.41 - 1.48: 1047 1.48 - 1.54: 2760 Bond restraints: 6900 Sorted by residual: bond pdb=" C GLN F 284 " pdb=" N PRO F 285 " ideal model delta sigma weight residual 1.329 1.338 -0.008 1.22e-02 6.72e+03 4.72e-01 bond pdb=" C GLN X 284 " pdb=" N PRO X 285 " ideal model delta sigma weight residual 1.329 1.338 -0.008 1.22e-02 6.72e+03 4.65e-01 bond pdb=" C GLN V 284 " pdb=" N PRO V 285 " ideal model delta sigma weight residual 1.329 1.337 -0.008 1.22e-02 6.72e+03 4.26e-01 bond pdb=" C GLN T 284 " pdb=" N PRO T 285 " ideal model delta sigma weight residual 1.329 1.337 -0.008 1.22e-02 6.72e+03 4.19e-01 bond pdb=" CB PRO 3 285 " pdb=" CG PRO 3 285 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.11e-01 ... (remaining 6895 not shown) Histogram of bond angle deviations from ideal: 102.11 - 107.32: 405 107.32 - 112.53: 2703 112.53 - 117.74: 1887 117.74 - 122.95: 3569 122.95 - 128.16: 796 Bond angle restraints: 9360 Sorted by residual: angle pdb=" CA PRO F 285 " pdb=" C PRO F 285 " pdb=" N GLN F 286 " ideal model delta sigma weight residual 114.58 116.46 -1.88 1.16e+00 7.43e-01 2.62e+00 angle pdb=" CA PRO H 285 " pdb=" C PRO H 285 " pdb=" N GLN H 286 " ideal model delta sigma weight residual 114.58 116.45 -1.87 1.16e+00 7.43e-01 2.59e+00 angle pdb=" CA PRO N 285 " pdb=" C PRO N 285 " pdb=" N GLN N 286 " ideal model delta sigma weight residual 114.58 116.45 -1.87 1.16e+00 7.43e-01 2.59e+00 angle pdb=" CA PRO P 285 " pdb=" C PRO P 285 " pdb=" N GLN P 286 " ideal model delta sigma weight residual 114.58 116.45 -1.87 1.16e+00 7.43e-01 2.59e+00 angle pdb=" CA PRO T 285 " pdb=" C PRO T 285 " pdb=" N GLN T 286 " ideal model delta sigma weight residual 114.58 116.45 -1.87 1.16e+00 7.43e-01 2.59e+00 ... (remaining 9355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3795 17.70 - 35.40: 165 35.40 - 53.10: 150 53.10 - 70.80: 30 70.80 - 88.50: 30 Dihedral angle restraints: 4170 sinusoidal: 1755 harmonic: 2415 Sorted by residual: dihedral pdb=" N GLN V 289 " pdb=" CA GLN V 289 " pdb=" CB GLN V 289 " pdb=" CG GLN V 289 " ideal model delta sinusoidal sigma weight residual -60.00 -92.51 32.51 3 1.50e+01 4.44e-03 5.36e+00 dihedral pdb=" N GLN 1 289 " pdb=" CA GLN 1 289 " pdb=" CB GLN 1 289 " pdb=" CG GLN 1 289 " ideal model delta sinusoidal sigma weight residual -60.00 -92.51 32.51 3 1.50e+01 4.44e-03 5.36e+00 dihedral pdb=" N GLN N 289 " pdb=" CA GLN N 289 " pdb=" CB GLN N 289 " pdb=" CG GLN N 289 " ideal model delta sinusoidal sigma weight residual -60.00 -92.49 32.49 3 1.50e+01 4.44e-03 5.36e+00 ... (remaining 4167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 393 0.024 - 0.047: 319 0.047 - 0.071: 67 0.071 - 0.094: 44 0.094 - 0.118: 32 Chirality restraints: 855 Sorted by residual: chirality pdb=" CA VAL G 269 " pdb=" N VAL G 269 " pdb=" C VAL G 269 " pdb=" CB VAL G 269 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA VAL C 269 " pdb=" N VAL C 269 " pdb=" C VAL C 269 " pdb=" CB VAL C 269 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA VAL U 269 " pdb=" N VAL U 269 " pdb=" C VAL U 269 " pdb=" CB VAL U 269 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 852 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR V 268 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C TYR V 268 " -0.020 2.00e-02 2.50e+03 pdb=" O TYR V 268 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL V 269 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR 3 268 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C TYR 3 268 " -0.020 2.00e-02 2.50e+03 pdb=" O TYR 3 268 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL 3 269 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 268 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C TYR F 268 " -0.020 2.00e-02 2.50e+03 pdb=" O TYR F 268 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL F 269 " 0.007 2.00e-02 2.50e+03 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1603 2.82 - 3.34: 5072 3.34 - 3.86: 11821 3.86 - 4.38: 14455 4.38 - 4.90: 23248 Nonbonded interactions: 56199 Sorted by model distance: nonbonded pdb=" O ALA B 274 " pdb=" OG SER B 277 " model vdw 2.300 2.440 nonbonded pdb=" O ALA V 274 " pdb=" OG SER V 277 " model vdw 2.301 2.440 nonbonded pdb=" O ALA X 274 " pdb=" OG SER X 277 " model vdw 2.301 2.440 nonbonded pdb=" O ALA Z 274 " pdb=" OG SER Z 277 " model vdw 2.301 2.440 nonbonded pdb=" O ALA T 274 " pdb=" OG SER T 277 " model vdw 2.301 2.440 ... (remaining 56194 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 '0' and resid 265 through 290) selection = chain '1' selection = (chain '2' and resid 265 through 290) selection = chain '3' selection = (chain 'A' and resid 265 through 290) selection = chain 'B' selection = (chain 'C' and resid 265 through 290) selection = chain 'D' selection = (chain 'E' and resid 265 through 290) selection = chain 'F' selection = (chain 'G' and resid 265 through 290) selection = chain 'H' selection = (chain 'I' and resid 265 through 290) selection = chain 'J' selection = (chain 'K' and resid 265 through 290) selection = chain 'L' selection = (chain 'M' and resid 265 through 290) selection = chain 'N' selection = (chain 'O' and resid 265 through 290) selection = chain 'P' selection = (chain 'Q' and resid 265 through 290) selection = chain 'R' selection = (chain 'S' and resid 265 through 290) selection = chain 'T' selection = (chain 'U' and resid 265 through 290) selection = chain 'V' selection = (chain 'W' and resid 265 through 290) selection = chain 'X' selection = (chain 'Y' and resid 265 through 290) selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 17.010 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 20.370 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 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 : 0.003 0.032 6900 Z= 0.201 Angle : 0.561 3.163 9360 Z= 0.321 Chirality : 0.040 0.118 855 Planarity : 0.007 0.026 1320 Dihedral : 17.773 88.500 2640 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.15), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.11), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE T 288 TYR 0.013 0.002 TYR Y 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.706 Fit side-chains REVERT: I 286 GLN cc_start: 0.9189 (mt0) cc_final: 0.8957 (mt0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 1.0124 time to fit residues: 91.7277 Evaluate side-chains 56 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 284 GLN ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 289 GLN C 278 GLN ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN D 289 GLN E 278 GLN E 284 GLN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 GLN F 289 GLN G 278 GLN G 284 GLN ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 GLN H 289 GLN ** I 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN I 284 GLN ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 271 GLN J 289 GLN K 278 GLN K 284 GLN ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 GLN L 289 GLN M 278 GLN ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 271 GLN N 289 GLN O 278 GLN O 284 GLN ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN P 289 GLN Q 278 GLN Q 284 GLN ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 GLN R 289 GLN S 278 GLN S 284 GLN ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN T 289 GLN U 278 GLN U 284 GLN ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN V 289 GLN W 278 GLN W 284 GLN ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 271 GLN X 289 GLN Y 278 GLN ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 271 GLN Z 289 GLN 0 278 GLN 0 284 GLN ** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 271 GLN 1 289 GLN 2 278 GLN 2 284 GLN 3 271 GLN 3 289 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.031 6900 Z= 0.497 Angle : 0.764 4.960 9360 Z= 0.454 Chirality : 0.049 0.159 855 Planarity : 0.006 0.040 1320 Dihedral : 5.966 15.576 885 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.63 % Allowed : 7.89 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.17), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.13), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE X 288 TYR 0.024 0.003 TYR E 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.808 Fit side-chains REVERT: A 289 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: C 289 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: E 263 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: I 286 GLN cc_start: 0.9319 (mt0) cc_final: 0.9003 (mt0) REVERT: M 289 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: O 263 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: 0 263 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8318 (mt0) outliers start: 12 outliers final: 3 residues processed: 73 average time/residue: 0.8832 time to fit residues: 69.7094 Evaluate side-chains 73 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain M residue 289 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain 0 residue 263 GLN Chi-restraints excluded: chain 1 residue 280 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 266 GLN ** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6900 Z= 0.200 Angle : 0.568 4.616 9360 Z= 0.327 Chirality : 0.044 0.140 855 Planarity : 0.005 0.034 1320 Dihedral : 5.243 16.062 885 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.50 % Allowed : 8.84 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE 0 288 TYR 0.021 0.002 TYR E 272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.830 Fit side-chains REVERT: A 289 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: C 263 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: I 286 GLN cc_start: 0.9271 (mt0) cc_final: 0.8976 (mt0) REVERT: M 263 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: O 263 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: 0 263 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8312 (mt0) outliers start: 11 outliers final: 1 residues processed: 75 average time/residue: 0.8615 time to fit residues: 69.9342 Evaluate side-chains 71 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain Y residue 277 SER Chi-restraints excluded: chain 0 residue 263 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 6900 Z= 0.286 Angle : 0.624 4.697 9360 Z= 0.363 Chirality : 0.046 0.151 855 Planarity : 0.005 0.034 1320 Dihedral : 5.473 15.932 885 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.04 % Allowed : 9.12 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE 3 288 TYR 0.022 0.002 TYR E 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.739 Fit side-chains REVERT: A 279 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: I 286 GLN cc_start: 0.9294 (mt0) cc_final: 0.9001 (mt0) REVERT: K 263 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: M 263 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: O 263 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: Z 266 GLN cc_start: 0.8920 (mt0) cc_final: 0.8678 (mt0) outliers start: 15 outliers final: 5 residues processed: 78 average time/residue: 0.7969 time to fit residues: 67.5280 Evaluate side-chains 78 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain K residue 263 GLN Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain Y residue 277 SER Chi-restraints excluded: chain 1 residue 280 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 6900 Z= 0.339 Angle : 0.654 4.663 9360 Z= 0.382 Chirality : 0.047 0.152 855 Planarity : 0.005 0.037 1320 Dihedral : 5.632 15.946 885 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.72 % Allowed : 8.98 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE X 288 TYR 0.023 0.002 TYR E 272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 70 time to evaluate : 0.797 Fit side-chains REVERT: A 279 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: E 263 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8221 (mt0) REVERT: G 289 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: K 263 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: O 263 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8154 (mt0) outliers start: 20 outliers final: 9 residues processed: 81 average time/residue: 0.7713 time to fit residues: 68.0473 Evaluate side-chains 84 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain G residue 289 GLN Chi-restraints excluded: chain I residue 273 SER Chi-restraints excluded: chain K residue 263 GLN Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain Y residue 277 SER Chi-restraints excluded: chain 1 residue 280 THR Chi-restraints excluded: chain 2 residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 6900 Z= 0.282 Angle : 0.618 4.529 9360 Z= 0.359 Chirality : 0.046 0.150 855 Planarity : 0.005 0.038 1320 Dihedral : 5.475 15.970 885 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.99 % Allowed : 8.98 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE 3 288 TYR 0.022 0.002 TYR E 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 72 time to evaluate : 0.899 Fit side-chains REVERT: A 279 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: C 263 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: E 263 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: I 279 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7471 (mp10) REVERT: K 263 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7856 (mp10) REVERT: O 263 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8135 (mt0) outliers start: 22 outliers final: 8 residues processed: 84 average time/residue: 0.8780 time to fit residues: 80.1564 Evaluate side-chains 83 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain K residue 263 GLN Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain Y residue 277 SER Chi-restraints excluded: chain 1 residue 280 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 6900 Z= 0.361 Angle : 0.662 4.691 9360 Z= 0.387 Chirality : 0.047 0.158 855 Planarity : 0.005 0.041 1320 Dihedral : 5.680 15.969 885 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.54 % Allowed : 8.16 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE 3 288 TYR 0.023 0.002 TYR I 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 0.815 Fit side-chains REVERT: A 263 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: C 263 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8317 (mt0) REVERT: E 263 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: E 279 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: G 289 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: I 279 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: K 263 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: O 263 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: 0 279 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8052 (mp10) outliers start: 26 outliers final: 12 residues processed: 89 average time/residue: 0.8528 time to fit residues: 82.0011 Evaluate side-chains 90 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain G residue 289 GLN Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain K residue 263 GLN Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain Y residue 277 SER Chi-restraints excluded: chain 0 residue 279 GLN Chi-restraints excluded: chain 1 residue 280 THR Chi-restraints excluded: chain 2 residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 0.0570 chunk 55 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6900 Z= 0.160 Angle : 0.536 4.590 9360 Z= 0.305 Chirality : 0.044 0.150 855 Planarity : 0.005 0.035 1320 Dihedral : 5.044 15.663 885 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.18 % Allowed : 9.80 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.19), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE W 288 TYR 0.023 0.002 TYR I 272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.789 Fit side-chains REVERT: A 263 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8226 (mt0) REVERT: C 263 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8214 (mt0) REVERT: E 263 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: I 279 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: M 263 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8088 (mt0) REVERT: O 263 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7763 (mt0) REVERT: 0 279 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8129 (mp10) outliers start: 16 outliers final: 5 residues processed: 83 average time/residue: 0.8468 time to fit residues: 76.0931 Evaluate side-chains 85 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain Y residue 277 SER Chi-restraints excluded: chain 0 residue 279 GLN Chi-restraints excluded: chain 1 residue 280 THR Chi-restraints excluded: chain 2 residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 GLN ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6900 Z= 0.217 Angle : 0.574 4.508 9360 Z= 0.330 Chirality : 0.045 0.149 855 Planarity : 0.005 0.033 1320 Dihedral : 5.189 15.730 885 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.04 % Allowed : 10.20 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.19), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE W 288 TYR 0.023 0.002 TYR I 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.834 Fit side-chains REVERT: A 263 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: C 263 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: E 263 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: I 279 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: 0 279 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8081 (mp10) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 0.7347 time to fit residues: 65.0153 Evaluate side-chains 86 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain Y residue 277 SER Chi-restraints excluded: chain 0 residue 279 GLN Chi-restraints excluded: chain 1 residue 280 THR Chi-restraints excluded: chain 2 residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 GLN ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 289 GLN ** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 289 GLN ** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 289 GLN ** Y 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 289 GLN ** 2 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 6900 Z= 0.310 Angle : 0.633 4.656 9360 Z= 0.368 Chirality : 0.046 0.152 855 Planarity : 0.005 0.037 1320 Dihedral : 5.514 15.871 885 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.31 % Allowed : 10.07 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.19), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE 3 288 TYR 0.024 0.002 TYR I 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 0.842 Fit side-chains REVERT: A 263 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: C 263 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: E 263 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: I 279 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.7567 (mp10) REVERT: O 263 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: 0 279 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8100 (mp10) outliers start: 17 outliers final: 10 residues processed: 80 average time/residue: 0.7366 time to fit residues: 64.4402 Evaluate side-chains 85 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain Y residue 277 SER Chi-restraints excluded: chain 0 residue 279 GLN Chi-restraints excluded: chain 1 residue 280 THR Chi-restraints excluded: chain 2 residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.074282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.062845 restraints weight = 10028.708| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.65 r_work: 0.2791 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 6900 Z= 0.332 Angle : 0.647 4.661 9360 Z= 0.377 Chirality : 0.046 0.153 855 Planarity : 0.005 0.039 1320 Dihedral : 5.594 15.933 885 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.31 % Allowed : 9.93 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE 3 288 TYR 0.023 0.002 TYR I 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2288.30 seconds wall clock time: 42 minutes 33.84 seconds (2553.84 seconds total)