Starting phenix.real_space_refine on Sat Nov 16 22:30:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c8r_45308/11_2024/9c8r_45308_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c8r_45308/11_2024/9c8r_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c8r_45308/11_2024/9c8r_45308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c8r_45308/11_2024/9c8r_45308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c8r_45308/11_2024/9c8r_45308_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c8r_45308/11_2024/9c8r_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-5513/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: 13.54, per 1000 atoms: 1.11 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: 2.78 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: 1.54 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: 4.17 Time building geometry restraints manager: 3.31 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: 1.960 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.910 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.570 ------------------------------------------------------------------------------- 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= 0.172 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 *********************** 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 : 1.290 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: 1.4474 time to fit residues: 222.1263 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 : 1.364 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 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= 0.301 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 *********************** 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 : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8165 (ttt-90) cc_final: 0.7939 (ttp80) REVERT: B 206 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8056 (mt-10) REVERT: B 394 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7138 (pt0) REVERT: C 221 LYS cc_start: 0.7767 (mttm) cc_final: 0.7068 (mtpt) REVERT: C 254 MET cc_start: 0.9262 (tpt) cc_final: 0.8936 (tpt) REVERT: C 323 ASP cc_start: 0.8341 (m-30) cc_final: 0.8133 (m-30) outliers start: 21 outliers final: 11 residues processed: 149 average time/residue: 1.4316 time to fit residues: 231.1773 Evaluate side-chains 137 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 116 ASN C 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12595 Z= 0.168 Angle : 0.495 5.381 17168 Z= 0.259 Chirality : 0.045 0.155 1796 Planarity : 0.005 0.042 2222 Dihedral : 4.278 28.493 1727 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.98 % Allowed : 12.89 % 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: 0.05 (0.21), residues: 1542 helix: 0.91 (0.23), residues: 521 sheet: -0.89 (0.33), residues: 213 loop : -0.18 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 262 HIS 0.003 0.001 HIS A 186 PHE 0.010 0.001 PHE A 426 TYR 0.017 0.001 TYR B 340 ARG 0.002 0.000 ARG B 85 *********************** 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 154 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 206 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7906 (mt-10) REVERT: C 221 LYS cc_start: 0.7738 (mttm) cc_final: 0.7025 (mtpt) REVERT: C 254 MET cc_start: 0.9274 (tpt) cc_final: 0.8990 (tpt) REVERT: C 323 ASP cc_start: 0.8326 (m-30) cc_final: 0.8115 (m-30) REVERT: C 386 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7103 (mt) outliers start: 23 outliers final: 11 residues processed: 147 average time/residue: 1.4457 time to fit residues: 229.5962 Evaluate side-chains 141 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 25 ASP 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 137 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12595 Z= 0.375 Angle : 0.584 6.038 17168 Z= 0.306 Chirality : 0.051 0.175 1796 Planarity : 0.005 0.046 2222 Dihedral : 4.495 32.136 1725 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: -0.15 (0.21), residues: 1542 helix: 0.74 (0.23), residues: 521 sheet: -0.98 (0.33), residues: 212 loop : -0.30 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 262 HIS 0.007 0.001 HIS A 186 PHE 0.013 0.002 PHE A 426 TYR 0.023 0.002 TYR B 340 ARG 0.004 0.000 ARG A 390 *********************** 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 158 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 SER cc_start: 0.8326 (p) cc_final: 0.7846 (t) REVERT: B 206 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 488 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7827 (tt0) REVERT: C 221 LYS cc_start: 0.7741 (mttm) cc_final: 0.7018 (mtpt) REVERT: C 254 MET cc_start: 0.9270 (tpt) cc_final: 0.8905 (tpt) REVERT: C 323 ASP cc_start: 0.8367 (m-30) cc_final: 0.8164 (m-30) outliers start: 21 outliers final: 13 residues processed: 153 average time/residue: 1.4231 time to fit residues: 235.5434 Evaluate side-chains 147 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 115 LYS 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 83 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 37 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12595 Z= 0.209 Angle : 0.516 5.966 17168 Z= 0.270 Chirality : 0.046 0.162 1796 Planarity : 0.005 0.050 2222 Dihedral : 4.353 29.833 1725 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.74 % Allowed : 13.44 % Favored : 84.82 % 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: -0.05 (0.21), residues: 1542 helix: 0.85 (0.23), residues: 521 sheet: -0.95 (0.33), residues: 212 loop : -0.26 (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 0.018 0.001 TYR B 340 ARG 0.002 0.000 ARG C 542 *********************** 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 155 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 SER cc_start: 0.8322 (p) cc_final: 0.7853 (t) REVERT: B 206 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7962 (mt-10) REVERT: B 488 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7818 (tt0) REVERT: C 221 LYS cc_start: 0.7727 (mttm) cc_final: 0.7004 (mtpt) REVERT: C 254 MET cc_start: 0.9275 (tpt) cc_final: 0.8943 (tpt) REVERT: C 323 ASP cc_start: 0.8352 (m-30) cc_final: 0.8136 (m-30) REVERT: C 401 ASP cc_start: 0.7467 (t0) cc_final: 0.7218 (t0) outliers start: 19 outliers final: 13 residues processed: 151 average time/residue: 1.5574 time to fit residues: 256.1472 Evaluate side-chains 151 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 133 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12595 Z= 0.259 Angle : 0.539 6.056 17168 Z= 0.281 Chirality : 0.048 0.168 1796 Planarity : 0.005 0.048 2222 Dihedral : 4.392 29.645 1725 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.06 % Allowed : 13.28 % Favored : 84.66 % 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: 0.84 (0.23), residues: 521 sheet: -0.99 (0.33), residues: 212 loop : -0.28 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 262 HIS 0.005 0.001 HIS A 186 PHE 0.011 0.001 PHE A 176 TYR 0.020 0.002 TYR B 340 ARG 0.003 0.000 ARG A 390 *********************** 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: 23 poor density : 135 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 SER cc_start: 0.8327 (p) cc_final: 0.7840 (t) REVERT: B 206 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7959 (mt-10) REVERT: B 488 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7812 (tt0) REVERT: C 221 LYS cc_start: 0.7724 (mttm) cc_final: 0.6997 (mtpt) REVERT: C 254 MET cc_start: 0.9282 (tpt) cc_final: 0.8919 (tpt) REVERT: C 323 ASP cc_start: 0.8370 (m-30) cc_final: 0.8161 (m-30) outliers start: 23 outliers final: 16 residues processed: 151 average time/residue: 1.3360 time to fit residues: 218.5013 Evaluate side-chains 149 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain C residue 440 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 147 optimal weight: 0.0970 chunk 92 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 68 optimal weight: 5.9990 chunk 91 optimal weight: 0.0970 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 HIS B 116 ASN C 112 HIS C 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12595 Z= 0.116 Angle : 0.464 6.959 17168 Z= 0.240 Chirality : 0.044 0.137 1796 Planarity : 0.005 0.050 2222 Dihedral : 4.069 22.060 1725 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.42 % Allowed : 14.39 % Favored : 84.19 % 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: 0.16 (0.22), residues: 1542 helix: 1.06 (0.23), residues: 521 sheet: -0.95 (0.33), residues: 220 loop : -0.11 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 262 HIS 0.002 0.001 HIS C 321 PHE 0.007 0.001 PHE C 426 TYR 0.013 0.001 TYR B 340 ARG 0.002 0.000 ARG B 494 *********************** 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: 15 poor density : 135 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7782 (tttm) cc_final: 0.7537 (tttp) REVERT: A 403 SER cc_start: 0.8264 (p) cc_final: 0.7789 (t) REVERT: B 206 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7698 (mt-10) REVERT: B 315 LYS cc_start: 0.8727 (tttt) cc_final: 0.8465 (tttp) REVERT: B 488 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7845 (tt0) REVERT: C 221 LYS cc_start: 0.7706 (mttm) cc_final: 0.6981 (mtpt) REVERT: C 254 MET cc_start: 0.9291 (tpt) cc_final: 0.8912 (tpt) REVERT: C 323 ASP cc_start: 0.8302 (m-30) cc_final: 0.8101 (m-30) REVERT: C 537 MET cc_start: 0.8558 (mmm) cc_final: 0.8355 (tpp) outliers start: 15 outliers final: 9 residues processed: 148 average time/residue: 1.4935 time to fit residues: 238.5340 Evaluate side-chains 143 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 392 MET 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 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.0170 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 134 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 12595 Z= 0.167 Angle : 0.732 59.199 17168 Z= 0.430 Chirality : 0.044 0.185 1796 Planarity : 0.005 0.048 2222 Dihedral : 4.038 18.824 1724 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.19 % Allowed : 14.70 % Favored : 84.11 % 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: 0.18 (0.22), residues: 1542 helix: 1.08 (0.23), residues: 521 sheet: -0.93 (0.33), residues: 220 loop : -0.10 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 262 HIS 0.005 0.001 HIS C 112 PHE 0.008 0.001 PHE C 426 TYR 0.013 0.001 TYR B 340 ARG 0.004 0.000 ARG A 390 *********************** 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 145 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7783 (tttm) cc_final: 0.7537 (tttp) REVERT: A 403 SER cc_start: 0.8243 (p) cc_final: 0.7791 (t) REVERT: B 116 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7557 (p0) REVERT: B 206 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 315 LYS cc_start: 0.8731 (tttt) cc_final: 0.8467 (tttp) REVERT: B 488 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7843 (tt0) REVERT: C 221 LYS cc_start: 0.7708 (mttm) cc_final: 0.6983 (mtpt) REVERT: C 254 MET cc_start: 0.9292 (tpt) cc_final: 0.8910 (tpt) REVERT: C 323 ASP cc_start: 0.8301 (m-30) cc_final: 0.8100 (m-30) REVERT: C 401 ASP cc_start: 0.7548 (t0) cc_final: 0.7300 (t0) REVERT: C 537 MET cc_start: 0.8558 (mmm) cc_final: 0.8344 (tpp) outliers start: 12 outliers final: 9 residues processed: 144 average time/residue: 1.4485 time to fit residues: 225.3563 Evaluate side-chains 142 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 392 MET 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 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 0.0030 chunk 141 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 12595 Z= 0.168 Angle : 0.720 55.056 17168 Z= 0.431 Chirality : 0.044 0.185 1796 Planarity : 0.005 0.048 2222 Dihedral : 4.038 18.824 1724 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.11 % Allowed : 14.70 % Favored : 84.19 % 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: 0.18 (0.22), residues: 1542 helix: 1.08 (0.23), residues: 521 sheet: -0.93 (0.33), residues: 220 loop : -0.10 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 262 HIS 0.005 0.001 HIS C 112 PHE 0.008 0.001 PHE C 426 TYR 0.013 0.001 TYR B 340 ARG 0.004 0.000 ARG A 390 *********************** 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 142 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7783 (tttm) cc_final: 0.7537 (tttp) REVERT: A 403 SER cc_start: 0.8243 (p) cc_final: 0.7790 (t) REVERT: B 206 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 315 LYS cc_start: 0.8730 (tttt) cc_final: 0.8467 (tttp) REVERT: B 488 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7843 (tt0) REVERT: C 221 LYS cc_start: 0.7710 (mttm) cc_final: 0.6983 (mtpt) REVERT: C 254 MET cc_start: 0.9292 (tpt) cc_final: 0.8910 (tpt) REVERT: C 323 ASP cc_start: 0.8302 (m-30) cc_final: 0.8100 (m-30) REVERT: C 401 ASP cc_start: 0.7549 (t0) cc_final: 0.7300 (t0) REVERT: C 537 MET cc_start: 0.8558 (mmm) cc_final: 0.8344 (tpp) outliers start: 11 outliers final: 9 residues processed: 141 average time/residue: 1.4500 time to fit residues: 220.8300 Evaluate side-chains 141 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 392 MET 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 397 VAL Chi-restraints excluded: chain B residue 411 VAL 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 145 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 101 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.003 0.103 12595 Z= 0.158 Angle : 0.731 59.193 17168 Z= 0.423 Chirality : 0.044 0.141 1796 Planarity : 0.005 0.047 2222 Dihedral : 4.035 18.824 1724 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.34 % Allowed : 14.47 % Favored : 84.19 % 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: 0.19 (0.22), residues: 1542 helix: 1.09 (0.23), residues: 521 sheet: -0.93 (0.33), residues: 220 loop : -0.10 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 262 HIS 0.005 0.001 HIS C 112 PHE 0.008 0.001 PHE C 426 TYR 0.014 0.001 TYR B 340 ARG 0.004 0.000 ARG A 390 ********************** 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 145 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7784 (tttm) cc_final: 0.7537 (tttp) REVERT: A 403 SER cc_start: 0.8260 (p) cc_final: 0.7799 (t) REVERT: B 206 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7741 (mt-10) REVERT: B 315 LYS cc_start: 0.8731 (tttt) cc_final: 0.8468 (tttp) REVERT: B 488 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7844 (tt0) REVERT: C 221 LYS cc_start: 0.7710 (mttm) cc_final: 0.6983 (mtpt) REVERT: C 254 MET cc_start: 0.9292 (tpt) cc_final: 0.8913 (tpt) REVERT: C 323 ASP cc_start: 0.8303 (m-30) cc_final: 0.8100 (m-30) REVERT: C 401 ASP cc_start: 0.7549 (t0) cc_final: 0.7299 (t0) REVERT: C 537 MET cc_start: 0.8559 (mmm) cc_final: 0.8345 (tpp) outliers start: 14 outliers final: 11 residues processed: 143 average time/residue: 1.4445 time to fit residues: 223.1178 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 : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 VAL 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 B residue 52 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 163 SER 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 129 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 106 optimal weight: 3.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- 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 = 0.116990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.087356 restraints weight = 45817.394| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 4.66 r_work: 0.2424 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2424 ------------------------------------------------------------------------------- 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 = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2411 r_free = 0.2411 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 12595 Z= 0.158 Angle : 0.731 59.193 17168 Z= 0.423 Chirality : 0.044 0.141 1796 Planarity : 0.005 0.047 2222 Dihedral : 4.035 18.824 1724 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.26 % Allowed : 14.55 % Favored : 84.19 % 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: 0.19 (0.22), residues: 1542 helix: 1.09 (0.23), residues: 521 sheet: -0.93 (0.33), residues: 220 loop : -0.10 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 262 HIS 0.005 0.001 HIS C 112 PHE 0.008 0.001 PHE C 426 TYR 0.014 0.001 TYR B 340 ARG 0.004 0.000 ARG A 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4417.51 seconds wall clock time: 89 minutes 52.40 seconds (5392.40 seconds total)