Starting phenix.real_space_refine on Tue Jun 10 23:45:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c8r_45308/06_2025/9c8r_45308_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c8r_45308/06_2025/9c8r_45308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c8r_45308/06_2025/9c8r_45308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c8r_45308/06_2025/9c8r_45308.map" model { file = "/net/cci-nas-00/data/ceres_data/9c8r_45308/06_2025/9c8r_45308_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c8r_45308/06_2025/9c8r_45308_neut.cif" } resolution = 2.83 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= 0.039 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 7822 2.51 5 N 2074 2.21 5 O 2255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12220 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 513, 4052 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 513, 4052 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 4157 Chain: "B" Number of atoms: 4068 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 512, 4049 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 477} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 512, 4049 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 477} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 4148 Chain: "C" Number of atoms: 4085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 519, 4071 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 484} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 519, 4071 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 484} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 4178 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALA A 191 " occ=0.82 ... (3 atoms not shown) pdb=" CB ALA A 191 " occ=0.82 residue: pdb=" N ALYS A 540 " occ=0.30 ... (16 atoms not shown) pdb=" NZ BLYS A 540 " occ=0.70 Time building chain proxies: 14.73, per 1000 atoms: 1.21 Number of scatterers: 12220 At special positions: 0 Unit cell: (126.38, 124.25, 74.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 2255 8.00 N 2074 7.00 C 7822 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 3.1 seconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 18 sheets defined 37.0% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.515A pdb=" N TYR A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 103 through 109 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 169 through 182 removed outlier: 4.178A pdb=" N ALA A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 174 " --> pdb=" O TRP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 262 through 268 removed outlier: 3.817A pdb=" N LYS A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.628A pdb=" N PHE A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'A' and resid 382 through 393 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 47 through 59 removed outlier: 3.600A pdb=" N TYR B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 59 " --> pdb=" O TRP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 75 removed outlier: 4.393A pdb=" N TRP B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 109 Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 137 through 154 Processing helix chain 'B' and resid 169 through 182 removed outlier: 4.177A pdb=" N ALA B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 174 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 224 through 234 Processing helix chain 'B' and resid 262 through 268 removed outlier: 3.826A pdb=" N LYS B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 318 removed outlier: 3.586A pdb=" N PHE B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.525A pdb=" N ILE B 341 " --> pdb=" O GLY B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 348 Processing helix chain 'B' and resid 365 through 375 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 507 through 516 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 63 through 75 Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 109 through 116 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.520A pdb=" N SER C 132 " --> pdb=" O PRO C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 154 Processing helix chain 'C' and resid 169 through 182 removed outlier: 4.269A pdb=" N ALA C 173 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 174 " --> pdb=" O TRP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 206 Processing helix chain 'C' and resid 224 through 234 removed outlier: 3.695A pdb=" N GLN C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 342 through 348 Processing helix chain 'C' and resid 365 through 375 Processing helix chain 'C' and resid 382 through 392 Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 507 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 136 removed outlier: 6.271A pdb=" N ALA A 121 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL A 354 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 123 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS A 328 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE A 355 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG A 325 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N TYR A 380 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA A 327 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 379 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 411 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR A 381 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.443A pdb=" N VAL A 209 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR A 213 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 162 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL A 189 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 164 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS A 186 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR A 288 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ALA A 188 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE A 285 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 503 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AA6, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.325A pdb=" N ASP A 527 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ALA A 493 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 525 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'B' and resid 133 through 136 removed outlier: 6.294A pdb=" N ALA B 121 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 354 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE B 123 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N CYS B 328 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE B 355 " --> pdb=" O CYS B 328 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG B 325 " --> pdb=" O GLN B 378 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N TYR B 380 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA B 327 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 379 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL B 411 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR B 381 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 408 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR B 437 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER B 410 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.471A pdb=" N VAL B 209 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR B 213 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 162 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 189 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 164 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N HIS B 186 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N TYR B 288 " --> pdb=" O HIS B 186 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA B 188 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B 285 " --> pdb=" O HIS B 301 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR B 503 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 216 through 218 Processing sheet with id=AB3, first strand: chain 'B' and resid 471 through 474 removed outlier: 5.268A pdb=" N ASP B 527 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ALA B 493 " --> pdb=" O PHE B 525 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE B 525 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY B 528 " --> pdb=" O LYS B 540 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB6, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.251A pdb=" N ALA C 121 " --> pdb=" O THR C 352 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL C 354 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE C 123 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N CYS C 328 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE C 355 " --> pdb=" O CYS C 328 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG C 325 " --> pdb=" O GLN C 378 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N TYR C 380 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA C 327 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 379 " --> pdb=" O GLY C 409 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL C 411 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR C 381 " --> pdb=" O VAL C 411 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 4.549A pdb=" N VAL C 209 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 213 " --> pdb=" O TYR C 165 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS C 186 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N TYR C 288 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ALA C 188 " --> pdb=" O TYR C 288 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS C 301 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 286 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL C 299 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR C 503 " --> pdb=" O VAL C 300 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 216 through 218 Processing sheet with id=AB9, first strand: chain 'C' and resid 471 through 474 removed outlier: 5.124A pdb=" N ASP C 527 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N ALA C 493 " --> pdb=" O PHE C 525 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 525 " --> pdb=" O ALA C 493 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 541 " --> pdb=" O GLY C 528 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA C 530 " --> pdb=" O ILE C 539 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE C 539 " --> pdb=" O ALA C 530 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1267 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: 4.51 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3937 1.34 - 1.46: 3122 1.46 - 1.58: 5431 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 12595 Sorted by residual: bond pdb=" N VAL B 397 " pdb=" CA VAL B 397 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.06e-02 8.90e+03 1.24e+01 bond pdb=" N ASN B 399 " pdb=" CA ASN B 399 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.86e+00 bond pdb=" N HIS B 400 " pdb=" CA HIS B 400 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.23e-02 6.61e+03 7.41e+00 bond pdb=" N LYS B 398 " pdb=" CA LYS B 398 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.21e-02 6.83e+03 6.77e+00 bond pdb=" N GLU B 394 " pdb=" CA GLU B 394 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.16e-02 7.43e+03 5.90e+00 ... (remaining 12590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 16851 1.73 - 3.46: 281 3.46 - 5.18: 31 5.18 - 6.91: 4 6.91 - 8.64: 1 Bond angle restraints: 17168 Sorted by residual: angle pdb=" N ASP B 395 " pdb=" CA ASP B 395 " pdb=" C ASP B 395 " ideal model delta sigma weight residual 112.88 107.72 5.16 1.29e+00 6.01e-01 1.60e+01 angle pdb=" N HIS B 396 " pdb=" CA HIS B 396 " pdb=" C HIS B 396 " ideal model delta sigma weight residual 113.72 108.76 4.96 1.30e+00 5.92e-01 1.46e+01 angle pdb=" N VAL B 397 " pdb=" CA VAL B 397 " pdb=" C VAL B 397 " ideal model delta sigma weight residual 112.12 109.61 2.51 8.40e-01 1.42e+00 8.96e+00 angle pdb=" CB MET B 33 " pdb=" CG MET B 33 " pdb=" SD MET B 33 " ideal model delta sigma weight residual 112.70 121.34 -8.64 3.00e+00 1.11e-01 8.29e+00 angle pdb=" C HIS B 400 " pdb=" CA HIS B 400 " pdb=" CB HIS B 400 " ideal model delta sigma weight residual 109.33 114.81 -5.48 1.97e+00 2.58e-01 7.74e+00 ... (remaining 17163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6638 17.78 - 35.55: 555 35.55 - 53.33: 158 53.33 - 71.10: 27 71.10 - 88.88: 19 Dihedral angle restraints: 7397 sinusoidal: 2904 harmonic: 4493 Sorted by residual: dihedral pdb=" CA LEU C 109 " pdb=" C LEU C 109 " pdb=" N ASP C 110 " pdb=" CA ASP C 110 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU A 109 " pdb=" C LEU A 109 " pdb=" N ASP A 110 " pdb=" CA ASP A 110 " ideal model delta harmonic sigma weight residual -180.00 -162.56 -17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB GLU A 49 " pdb=" CG GLU A 49 " pdb=" CD GLU A 49 " pdb=" OE1 GLU A 49 " ideal model delta sinusoidal sigma weight residual 0.00 88.88 -88.88 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1342 0.045 - 0.089: 312 0.089 - 0.134: 137 0.134 - 0.178: 3 0.178 - 0.223: 2 Chirality restraints: 1796 Sorted by residual: chirality pdb=" CB VAL B 397 " pdb=" CA VAL B 397 " pdb=" CG1 VAL B 397 " pdb=" CG2 VAL B 397 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA VAL B 397 " pdb=" N VAL B 397 " pdb=" C VAL B 397 " pdb=" CB VAL B 397 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE C 286 " pdb=" N ILE C 286 " pdb=" C ILE C 286 " pdb=" CB ILE C 286 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1793 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 416 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 417 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 417 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 417 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 30 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO C 31 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 31 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 31 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 363 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 364 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 364 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 364 " -0.023 5.00e-02 4.00e+02 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1686 2.76 - 3.29: 10998 3.29 - 3.83: 21497 3.83 - 4.36: 26361 4.36 - 4.90: 44395 Nonbonded interactions: 104937 Sorted by model distance: nonbonded pdb=" OE2 GLU A 442 " pdb=" OH TYR A 515 " model vdw 2.220 3.040 nonbonded pdb=" NZ LYS C 297 " pdb=" OH TYR C 515 " model vdw 2.221 3.120 nonbonded pdb=" OG SER B 63 " pdb=" NH2 ARG B 85 " model vdw 2.265 3.120 nonbonded pdb=" OE2 GLU B 442 " pdb=" OH TYR B 515 " model vdw 2.273 3.040 nonbonded pdb=" O HIS A 400 " pdb=" NZ LYS A 429 " model vdw 2.293 3.120 ... (remaining 104932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 61 or (resid 62 and (name N or nam \ e CA or name C or name O or name CB )) or resid 63 through 220 or (resid 221 and \ (name N or name CA or name C or name O or name CB )) or resid 222 through 226 o \ r resid 228 through 290 or (resid 295 and (name N or name CA or name C or name O \ or name CB )) or resid 296 through 324 or resid 326 through 372 or resid 374 th \ rough 383 or resid 385 through 420 or resid 422 through 494 or (resid 495 and (n \ ame N or name CA or name C or name O or name CB )) or resid 496 through 508 or ( \ resid 509 and (name N or name CA or name C or name O or name CB )) or resid 510 \ through 539 or resid 541)) selection = (chain 'B' and (resid 26 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 226 or resid 228 through 250 or (r \ esid 251 and (name N or name CA or name C or name O or name CB )) or resid 252 t \ hrough 290 or (resid 295 and (name N or name CA or name C or name O or name CB ) \ ) or resid 296 through 324 or resid 326 through 372 or resid 374 through 383 or \ resid 385 through 420 or resid 422 through 482 or (resid 483 and (name N or name \ CA or name C or name O or name CB )) or resid 484 through 494 or (resid 495 and \ (name N or name CA or name C or name O or name CB )) or resid 496 through 508 o \ r (resid 509 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 10 through 539 or resid 541)) selection = (chain 'C' and (resid 26 through 220 or (resid 221 and (name N or name CA or nam \ e C or name O or name CB )) or resid 222 through 226 or resid 228 through 290 or \ resid 295 through 324 or resid 326 through 372 or resid 374 through 383 or resi \ d 385 through 420 or resid 422 through 539 or resid 541)) } 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=0.07 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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 42.030 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 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 0.037 12595 Z= 0.144 Angle : 0.552 8.640 17168 Z= 0.317 Chirality : 0.045 0.223 1796 Planarity : 0.005 0.044 2222 Dihedral : 15.123 88.878 4541 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.95 % Allowed : 13.68 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.07 (0.21), residues: 1542 helix: 0.56 (0.23), residues: 512 sheet: -0.73 (0.36), residues: 192 loop : -0.15 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 262 HIS 0.003 0.001 HIS C 421 PHE 0.008 0.001 PHE C 355 TYR 0.018 0.001 TYR B 340 ARG 0.003 0.000 ARG B 494 Details of bonding type rmsd hydrogen bonds : bond 0.16167 ( 456) hydrogen bonds : angle 6.82237 ( 1267) covalent geometry : bond 0.00265 (12595) covalent geometry : angle 0.55184 (17168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8034 (ttt-90) cc_final: 0.7733 (mtp180) REVERT: A 440 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8760 (ptm) REVERT: B 206 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 315 LYS cc_start: 0.8723 (tttt) cc_final: 0.8439 (tttp) REVERT: B 394 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7337 (pt0) REVERT: B 403 SER cc_start: 0.8278 (p) cc_final: 0.7776 (t) REVERT: C 53 LYS cc_start: 0.7720 (tttp) cc_final: 0.7140 (tttm) REVERT: C 221 LYS cc_start: 0.7759 (mttm) cc_final: 0.7074 (mtpt) REVERT: C 254 MET cc_start: 0.9271 (tpt) cc_final: 0.8913 (tpt) outliers start: 11 outliers final: 5 residues processed: 142 average time/residue: 1.5026 time to fit residues: 230.5758 Evaluate side-chains 130 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 0.0670 chunk 39 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 0.0370 chunk 138 optimal weight: 6.9990 overall best weight: 2.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 421 HIS B 116 ASN C 116 ASN C 421 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.113207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.080947 restraints weight = 31106.815| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.08 r_work: 0.2448 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2412 r_free = 0.2412 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2412 r_free = 0.2412 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12595 Z= 0.187 Angle : 0.570 6.666 17168 Z= 0.300 Chirality : 0.049 0.174 1796 Planarity : 0.005 0.046 2222 Dihedral : 4.840 51.364 1735 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.82 % Allowed : 12.65 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.08 (0.21), residues: 1542 helix: 0.73 (0.23), residues: 521 sheet: -0.97 (0.33), residues: 213 loop : -0.21 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 262 HIS 0.006 0.001 HIS A 186 PHE 0.012 0.002 PHE A 176 TYR 0.022 0.002 TYR B 340 ARG 0.003 0.000 ARG C 390 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 456) hydrogen bonds : angle 5.34375 ( 1267) covalent geometry : bond 0.00468 (12595) covalent geometry : angle 0.57009 (17168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8154 (ttt-90) cc_final: 0.7928 (ttp80) REVERT: B 206 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8167 (mt-10) REVERT: B 403 SER cc_start: 0.8423 (p) cc_final: 0.8211 (p) REVERT: C 221 LYS cc_start: 0.8009 (mttm) cc_final: 0.7376 (mtpt) REVERT: C 254 MET cc_start: 0.9298 (tpt) cc_final: 0.8997 (tpt) outliers start: 21 outliers final: 11 residues processed: 149 average time/residue: 1.3351 time to fit residues: 217.0646 Evaluate side-chains 138 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 13 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 116 ASN A 421 HIS B 112 HIS B 116 ASN C 112 HIS C 116 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.116604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.086013 restraints weight = 40754.235| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 4.11 r_work: 0.2427 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2411 r_free = 0.2411 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2411 r_free = 0.2411 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12595 Z= 0.097 Angle : 0.480 5.299 17168 Z= 0.251 Chirality : 0.045 0.149 1796 Planarity : 0.004 0.042 2222 Dihedral : 4.203 26.899 1727 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.82 % Allowed : 13.04 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.10 (0.21), residues: 1542 helix: 0.95 (0.23), residues: 521 sheet: -0.85 (0.33), residues: 213 loop : -0.15 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 262 HIS 0.002 0.001 HIS C 338 PHE 0.009 0.001 PHE A 426 TYR 0.015 0.001 TYR B 340 ARG 0.003 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 456) hydrogen bonds : angle 4.98949 ( 1267) covalent geometry : bond 0.00219 (12595) covalent geometry : angle 0.47953 (17168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8147 (ttt-90) cc_final: 0.7871 (ttp80) REVERT: B 206 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 403 SER cc_start: 0.8428 (p) cc_final: 0.8140 (p) REVERT: C 221 LYS cc_start: 0.7994 (mttm) cc_final: 0.7336 (mtpt) REVERT: C 254 MET cc_start: 0.9320 (tpt) cc_final: 0.8961 (tpt) REVERT: C 386 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7305 (mt) outliers start: 21 outliers final: 10 residues processed: 143 average time/residue: 1.3426 time to fit residues: 208.1407 Evaluate side-chains 140 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 95 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 112 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 116 ASN C 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.109353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.079225 restraints weight = 39290.246| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.77 r_work: 0.2395 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2371 r_free = 0.2371 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2371 r_free = 0.2371 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12595 Z= 0.241 Angle : 0.594 6.052 17168 Z= 0.311 Chirality : 0.051 0.176 1796 Planarity : 0.005 0.047 2222 Dihedral : 4.502 32.026 1725 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.82 % Allowed : 13.28 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.12 (0.21), residues: 1542 helix: 0.75 (0.23), residues: 521 sheet: -1.00 (0.33), residues: 212 loop : -0.27 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 262 HIS 0.007 0.001 HIS A 186 PHE 0.013 0.002 PHE C 176 TYR 0.024 0.002 TYR B 340 ARG 0.003 0.000 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.05362 ( 456) hydrogen bonds : angle 5.23586 ( 1267) covalent geometry : bond 0.00608 (12595) covalent geometry : angle 0.59419 (17168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8097 (mt-10) REVERT: B 403 SER cc_start: 0.8368 (p) cc_final: 0.7767 (t) REVERT: B 488 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7862 (tt0) REVERT: C 221 LYS cc_start: 0.7902 (mttm) cc_final: 0.7215 (mtpt) outliers start: 21 outliers final: 12 residues processed: 151 average time/residue: 1.3838 time to fit residues: 226.1765 Evaluate side-chains 143 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 125 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN C 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.113487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.084987 restraints weight = 47888.116| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 5.17 r_work: 0.2420 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2348 r_free = 0.2348 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2348 r_free = 0.2348 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12595 Z= 0.137 Angle : 0.519 5.594 17168 Z= 0.271 Chirality : 0.047 0.162 1796 Planarity : 0.005 0.053 2222 Dihedral : 4.363 30.153 1725 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.66 % Allowed : 13.28 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.03 (0.21), residues: 1542 helix: 0.84 (0.23), residues: 521 sheet: -0.97 (0.33), residues: 212 loop : -0.22 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 262 HIS 0.004 0.001 HIS A 186 PHE 0.011 0.001 PHE A 176 TYR 0.019 0.001 TYR B 340 ARG 0.002 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 456) hydrogen bonds : angle 5.06544 ( 1267) covalent geometry : bond 0.00334 (12595) covalent geometry : angle 0.51899 (17168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8140 (mt-10) REVERT: B 403 SER cc_start: 0.8400 (p) cc_final: 0.7793 (t) REVERT: B 488 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7959 (tt0) REVERT: C 221 LYS cc_start: 0.7993 (mttm) cc_final: 0.7322 (mtpt) REVERT: C 254 MET cc_start: 0.9335 (tpt) cc_final: 0.9062 (tpt) outliers start: 18 outliers final: 13 residues processed: 150 average time/residue: 1.7208 time to fit residues: 279.9719 Evaluate side-chains 150 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 66 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 35 optimal weight: 0.0970 chunk 136 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN C 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.082219 restraints weight = 32518.231| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.23 r_work: 0.2431 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2411 r_free = 0.2411 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2411 r_free = 0.2411 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12595 Z= 0.124 Angle : 0.502 5.700 17168 Z= 0.262 Chirality : 0.046 0.157 1796 Planarity : 0.005 0.049 2222 Dihedral : 4.250 26.777 1725 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.90 % Allowed : 13.52 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.06 (0.21), residues: 1542 helix: 0.93 (0.23), residues: 521 sheet: -0.90 (0.33), residues: 212 loop : -0.19 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 262 HIS 0.004 0.001 HIS A 186 PHE 0.011 0.001 PHE A 426 TYR 0.017 0.001 TYR B 340 ARG 0.002 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 456) hydrogen bonds : angle 4.95053 ( 1267) covalent geometry : bond 0.00300 (12595) covalent geometry : angle 0.50248 (17168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 SER cc_start: 0.8449 (p) cc_final: 0.7945 (t) REVERT: B 206 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 403 SER cc_start: 0.8395 (p) cc_final: 0.7776 (t) REVERT: B 488 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7911 (tt0) REVERT: C 221 LYS cc_start: 0.7977 (mttm) cc_final: 0.7293 (mtpt) REVERT: C 254 MET cc_start: 0.9319 (tpt) cc_final: 0.9028 (tpt) outliers start: 21 outliers final: 14 residues processed: 152 average time/residue: 1.5381 time to fit residues: 253.8354 Evaluate side-chains 145 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 chunk 138 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 33 optimal weight: 0.0670 overall best weight: 1.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN C 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.113678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.081723 restraints weight = 33087.127| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.26 r_work: 0.2425 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2414 r_free = 0.2414 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2414 r_free = 0.2414 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12595 Z= 0.118 Angle : 0.498 6.921 17168 Z= 0.259 Chirality : 0.046 0.156 1796 Planarity : 0.005 0.050 2222 Dihedral : 4.193 24.800 1725 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.74 % Allowed : 13.75 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.08 (0.22), residues: 1542 helix: 0.97 (0.23), residues: 521 sheet: -0.92 (0.33), residues: 213 loop : -0.19 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 262 HIS 0.004 0.001 HIS B 186 PHE 0.010 0.001 PHE A 176 TYR 0.017 0.001 TYR B 340 ARG 0.002 0.000 ARG B 494 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 456) hydrogen bonds : angle 4.91264 ( 1267) covalent geometry : bond 0.00284 (12595) covalent geometry : angle 0.49787 (17168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7870 (tttm) cc_final: 0.7610 (tttp) REVERT: A 221 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7151 (mtpt) REVERT: A 390 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7875 (ttp80) REVERT: A 403 SER cc_start: 0.8472 (p) cc_final: 0.7977 (t) REVERT: B 206 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7952 (mt-10) REVERT: B 403 SER cc_start: 0.8321 (p) cc_final: 0.7697 (t) REVERT: B 488 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7947 (tt0) REVERT: C 221 LYS cc_start: 0.7986 (mttm) cc_final: 0.7310 (mtpt) REVERT: C 254 MET cc_start: 0.9308 (tpt) cc_final: 0.8988 (tpt) outliers start: 19 outliers final: 12 residues processed: 146 average time/residue: 1.9176 time to fit residues: 301.6985 Evaluate side-chains 143 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 109 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN C 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.116752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.084968 restraints weight = 30914.742| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.04 r_work: 0.2496 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12595 Z= 0.085 Angle : 0.462 5.386 17168 Z= 0.239 Chirality : 0.044 0.141 1796 Planarity : 0.005 0.048 2222 Dihedral : 4.001 20.697 1725 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.19 % Allowed : 14.47 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.21 (0.22), residues: 1542 helix: 1.12 (0.23), residues: 521 sheet: -0.88 (0.33), residues: 220 loop : -0.11 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 262 HIS 0.002 0.001 HIS C 186 PHE 0.008 0.001 PHE C 426 TYR 0.014 0.001 TYR B 340 ARG 0.001 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 456) hydrogen bonds : angle 4.73688 ( 1267) covalent geometry : bond 0.00190 (12595) covalent geometry : angle 0.46196 (17168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.6768 (mp0) cc_final: 0.6481 (tp30) REVERT: A 53 LYS cc_start: 0.7897 (tttm) cc_final: 0.7671 (tttp) REVERT: A 206 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7942 (mt-10) REVERT: A 221 LYS cc_start: 0.7948 (mmtt) cc_final: 0.7184 (mtpt) REVERT: A 390 ARG cc_start: 0.8136 (ttt-90) cc_final: 0.7805 (ttp80) REVERT: A 403 SER cc_start: 0.8440 (p) cc_final: 0.7933 (t) REVERT: B 206 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 315 LYS cc_start: 0.8879 (tttt) cc_final: 0.8632 (tttp) REVERT: B 403 SER cc_start: 0.8303 (p) cc_final: 0.7693 (t) REVERT: B 488 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7926 (tt0) REVERT: C 221 LYS cc_start: 0.7992 (mttm) cc_final: 0.7320 (mtpt) REVERT: C 254 MET cc_start: 0.9311 (tpt) cc_final: 0.9058 (tpt) REVERT: C 401 ASP cc_start: 0.7732 (t0) cc_final: 0.7528 (t0) REVERT: C 537 MET cc_start: 0.8789 (mmm) cc_final: 0.8536 (tpp) outliers start: 12 outliers final: 8 residues processed: 151 average time/residue: 1.4389 time to fit residues: 234.6621 Evaluate side-chains 144 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 36 optimal weight: 0.0970 chunk 141 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 0.2980 chunk 129 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN C 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.116575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.085777 restraints weight = 39539.125| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.77 r_work: 0.2438 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2429 r_free = 0.2429 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2429 r_free = 0.2429 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12595 Z= 0.097 Angle : 0.476 5.770 17168 Z= 0.246 Chirality : 0.044 0.147 1796 Planarity : 0.005 0.044 2222 Dihedral : 3.958 19.276 1724 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.26 % Allowed : 15.02 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.25 (0.22), residues: 1542 helix: 1.14 (0.23), residues: 521 sheet: -0.84 (0.33), residues: 220 loop : -0.08 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 262 HIS 0.003 0.001 HIS A 186 PHE 0.009 0.001 PHE A 176 TYR 0.015 0.001 TYR B 340 ARG 0.003 0.000 ARG B 494 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 456) hydrogen bonds : angle 4.74037 ( 1267) covalent geometry : bond 0.00227 (12595) covalent geometry : angle 0.47597 (17168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.6771 (mp0) cc_final: 0.6460 (tp30) REVERT: A 53 LYS cc_start: 0.7882 (tttm) cc_final: 0.7663 (tttp) REVERT: A 206 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8004 (mt-10) REVERT: A 221 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7138 (mtpt) REVERT: A 390 ARG cc_start: 0.8135 (ttt-90) cc_final: 0.7813 (ttp80) REVERT: A 403 SER cc_start: 0.8413 (p) cc_final: 0.7942 (t) REVERT: B 206 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 315 LYS cc_start: 0.8902 (tttt) cc_final: 0.8666 (tttp) REVERT: B 403 SER cc_start: 0.8213 (p) cc_final: 0.7651 (t) REVERT: B 488 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7970 (tt0) REVERT: C 221 LYS cc_start: 0.8013 (mttm) cc_final: 0.7321 (mtpt) REVERT: C 254 MET cc_start: 0.9311 (tpt) cc_final: 0.9033 (tpt) REVERT: C 401 ASP cc_start: 0.7766 (t0) cc_final: 0.7560 (t0) REVERT: C 537 MET cc_start: 0.8824 (mmm) cc_final: 0.8566 (tpp) outliers start: 13 outliers final: 8 residues processed: 143 average time/residue: 1.8576 time to fit residues: 287.0484 Evaluate side-chains 142 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 68 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 127 optimal weight: 0.0670 chunk 49 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN C 116 ASN C 424 ASN C 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.116421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.087102 restraints weight = 45023.301| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 4.68 r_work: 0.2426 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2410 r_free = 0.2410 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2410 r_free = 0.2410 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12595 Z= 0.093 Angle : 0.473 6.066 17168 Z= 0.243 Chirality : 0.044 0.146 1796 Planarity : 0.005 0.045 2222 Dihedral : 3.935 19.280 1724 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.11 % Allowed : 15.02 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1542 helix: 1.18 (0.23), residues: 521 sheet: -0.83 (0.33), residues: 220 loop : -0.06 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 262 HIS 0.002 0.001 HIS A 186 PHE 0.009 0.001 PHE A 176 TYR 0.015 0.001 TYR B 340 ARG 0.002 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 456) hydrogen bonds : angle 4.70249 ( 1267) covalent geometry : bond 0.00215 (12595) covalent geometry : angle 0.47302 (17168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.6806 (mp0) cc_final: 0.6470 (tp30) REVERT: A 53 LYS cc_start: 0.7881 (tttm) cc_final: 0.7668 (tttp) REVERT: A 206 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8013 (mt-10) REVERT: A 221 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7126 (mtpt) REVERT: A 403 SER cc_start: 0.8398 (p) cc_final: 0.7936 (t) REVERT: B 206 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7943 (mt-10) REVERT: B 315 LYS cc_start: 0.8925 (tttt) cc_final: 0.8697 (tttp) REVERT: B 403 SER cc_start: 0.8158 (p) cc_final: 0.7650 (t) REVERT: B 488 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7989 (tt0) REVERT: C 221 LYS cc_start: 0.7989 (mttm) cc_final: 0.7284 (mtpt) REVERT: C 254 MET cc_start: 0.9347 (tpt) cc_final: 0.9023 (tpt) REVERT: C 401 ASP cc_start: 0.7786 (t0) cc_final: 0.7584 (t0) outliers start: 11 outliers final: 11 residues processed: 144 average time/residue: 1.5789 time to fit residues: 247.2766 Evaluate side-chains 143 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 138 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 7 optimal weight: 0.0670 chunk 88 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN C 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.116989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.086991 restraints weight = 42629.995| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.30 r_work: 0.2429 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2413 r_free = 0.2413 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2413 r_free = 0.2413 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12595 Z= 0.098 Angle : 0.475 6.719 17168 Z= 0.245 Chirality : 0.044 0.147 1796 Planarity : 0.005 0.044 2222 Dihedral : 3.939 19.375 1724 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.19 % Allowed : 15.10 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1542 helix: 1.16 (0.23), residues: 521 sheet: -0.82 (0.33), residues: 220 loop : -0.06 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 262 HIS 0.003 0.001 HIS A 186 PHE 0.009 0.001 PHE A 176 TYR 0.015 0.001 TYR B 340 ARG 0.006 0.000 ARG B 494 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 456) hydrogen bonds : angle 4.70259 ( 1267) covalent geometry : bond 0.00229 (12595) covalent geometry : angle 0.47532 (17168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9547.71 seconds wall clock time: 170 minutes 43.85 seconds (10243.85 seconds total)