Starting phenix.real_space_refine on Mon Jan 20 02:30:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5h_19735/01_2025/8s5h_19735_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5h_19735/01_2025/8s5h_19735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s5h_19735/01_2025/8s5h_19735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5h_19735/01_2025/8s5h_19735.map" model { file = "/net/cci-nas-00/data/ceres_data/8s5h_19735/01_2025/8s5h_19735_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5h_19735/01_2025/8s5h_19735_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.145 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: 7 Type Number sf(0) Gaussians Fe 8 7.16 5 P 8 5.49 5 S 176 5.16 5 C 20216 2.51 5 N 5536 2.21 5 O 5960 1.98 5 H 31936 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 63840 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7937 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 19.68, per 1000 atoms: 0.31 Number of scatterers: 63840 At special positions: 0 Unit cell: (152.985, 150.815, 254.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 S 176 16.00 P 8 15.00 O 5960 8.00 N 5536 7.00 C 20216 6.00 H 31936 1.00 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.25 Conformation dependent library (CDL) restraints added in 4.5 seconds 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7456 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 38 sheets defined 45.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 119 through 133 Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.866A pdb=" N HIS A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 258 through 272 removed outlier: 4.308A pdb=" N ILE A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.714A pdb=" N VAL A 319 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 343 Processing helix chain 'A' and resid 347 through 361 removed outlier: 3.714A pdb=" N LYS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.882A pdb=" N ASN A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 398 through 404 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.794A pdb=" N LYS A 481 " --> pdb=" O GLN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 99 removed outlier: 4.133A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 119 through 133 Processing helix chain 'B' and resid 148 through 162 Processing helix chain 'B' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 226 through 235 removed outlier: 3.867A pdb=" N HIS B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 258 through 272 removed outlier: 4.307A pdb=" N ILE B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.712A pdb=" N VAL B 319 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 343 Processing helix chain 'B' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.884A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 394 Processing helix chain 'B' and resid 398 through 404 Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.794A pdb=" N LYS B 481 " --> pdb=" O GLN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 119 through 133 Processing helix chain 'C' and resid 148 through 162 Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.867A pdb=" N HIS C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 258 through 272 removed outlier: 4.308A pdb=" N ILE C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.713A pdb=" N VAL C 319 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 343 Processing helix chain 'C' and resid 347 through 361 removed outlier: 3.714A pdb=" N LYS C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.883A pdb=" N ASN C 380 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET C 382 " --> pdb=" O ARG C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 394 Processing helix chain 'C' and resid 398 through 404 Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 430 through 441 Processing helix chain 'C' and resid 461 through 470 Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.794A pdb=" N LYS C 481 " --> pdb=" O GLN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 535 through 548 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS D 97 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 148 through 162 Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 226 through 235 removed outlier: 3.866A pdb=" N HIS D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 Processing helix chain 'D' and resid 258 through 272 removed outlier: 4.309A pdb=" N ILE D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.713A pdb=" N VAL D 319 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 343 Processing helix chain 'D' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 377 through 382 removed outlier: 3.883A pdb=" N ASN D 380 " --> pdb=" O SER D 377 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET D 382 " --> pdb=" O ARG D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 394 Processing helix chain 'D' and resid 398 through 404 Processing helix chain 'D' and resid 413 through 417 Processing helix chain 'D' and resid 430 through 441 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.794A pdb=" N LYS D 481 " --> pdb=" O GLN D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 535 through 548 Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 93 through 99 removed outlier: 4.133A pdb=" N LYS E 97 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE E 99 " --> pdb=" O ILE E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 148 through 162 Processing helix chain 'E' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 214 Processing helix chain 'E' and resid 226 through 235 removed outlier: 3.867A pdb=" N HIS E 232 " --> pdb=" O ASN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 244 Processing helix chain 'E' and resid 258 through 272 removed outlier: 4.308A pdb=" N ILE E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 316 through 320 removed outlier: 3.714A pdb=" N VAL E 319 " --> pdb=" O ASP E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 343 Processing helix chain 'E' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS E 359 " --> pdb=" O ALA E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 377 through 382 removed outlier: 3.883A pdb=" N ASN E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET E 382 " --> pdb=" O ARG E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 394 Processing helix chain 'E' and resid 398 through 404 Processing helix chain 'E' and resid 413 through 417 Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'E' and resid 478 through 482 removed outlier: 3.793A pdb=" N LYS E 481 " --> pdb=" O GLN E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 535 through 548 Processing helix chain 'F' and resid 59 through 63 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS F 97 " --> pdb=" O ASN F 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 119 through 133 Processing helix chain 'F' and resid 148 through 162 Processing helix chain 'F' and resid 174 through 184 removed outlier: 3.782A pdb=" N VAL F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 214 Processing helix chain 'F' and resid 226 through 235 removed outlier: 3.867A pdb=" N HIS F 232 " --> pdb=" O ASN F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 244 Processing helix chain 'F' and resid 258 through 272 removed outlier: 4.308A pdb=" N ILE F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.713A pdb=" N VAL F 319 " --> pdb=" O ASP F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 343 Processing helix chain 'F' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 377 through 382 removed outlier: 3.883A pdb=" N ASN F 380 " --> pdb=" O SER F 377 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET F 382 " --> pdb=" O ARG F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 394 Processing helix chain 'F' and resid 398 through 404 Processing helix chain 'F' and resid 413 through 417 Processing helix chain 'F' and resid 430 through 441 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'F' and resid 478 through 482 removed outlier: 3.793A pdb=" N LYS F 481 " --> pdb=" O GLN F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 504 Processing helix chain 'F' and resid 535 through 548 Processing helix chain 'G' and resid 59 through 63 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE G 99 " --> pdb=" O ILE G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 119 through 133 Processing helix chain 'G' and resid 148 through 162 Processing helix chain 'G' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 Processing helix chain 'G' and resid 226 through 235 removed outlier: 3.867A pdb=" N HIS G 232 " --> pdb=" O ASN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 244 Processing helix chain 'G' and resid 258 through 272 removed outlier: 4.309A pdb=" N ILE G 264 " --> pdb=" O THR G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 295 Processing helix chain 'G' and resid 316 through 320 removed outlier: 3.713A pdb=" N VAL G 319 " --> pdb=" O ASP G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 343 Processing helix chain 'G' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 377 through 382 removed outlier: 3.883A pdb=" N ASN G 380 " --> pdb=" O SER G 377 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET G 382 " --> pdb=" O ARG G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 394 Processing helix chain 'G' and resid 398 through 404 Processing helix chain 'G' and resid 413 through 417 Processing helix chain 'G' and resid 430 through 441 Processing helix chain 'G' and resid 461 through 470 Processing helix chain 'G' and resid 478 through 482 removed outlier: 3.793A pdb=" N LYS G 481 " --> pdb=" O GLN G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 495 through 504 Processing helix chain 'G' and resid 535 through 548 Processing helix chain 'H' and resid 59 through 63 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 93 through 99 removed outlier: 4.132A pdb=" N LYS H 97 " --> pdb=" O ASN H 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE H 99 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'H' and resid 119 through 133 Processing helix chain 'H' and resid 148 through 162 Processing helix chain 'H' and resid 174 through 184 removed outlier: 3.781A pdb=" N VAL H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 214 Processing helix chain 'H' and resid 226 through 235 removed outlier: 3.866A pdb=" N HIS H 232 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 244 Processing helix chain 'H' and resid 258 through 272 removed outlier: 4.308A pdb=" N ILE H 264 " --> pdb=" O THR H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 295 Processing helix chain 'H' and resid 316 through 320 removed outlier: 3.713A pdb=" N VAL H 319 " --> pdb=" O ASP H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 343 Processing helix chain 'H' and resid 347 through 361 removed outlier: 3.713A pdb=" N LYS H 359 " --> pdb=" O ALA H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 364 No H-bonds generated for 'chain 'H' and resid 362 through 364' Processing helix chain 'H' and resid 377 through 382 removed outlier: 3.882A pdb=" N ASN H 380 " --> pdb=" O SER H 377 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET H 382 " --> pdb=" O ARG H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 394 Processing helix chain 'H' and resid 398 through 404 Processing helix chain 'H' and resid 413 through 417 Processing helix chain 'H' and resid 430 through 441 Processing helix chain 'H' and resid 461 through 470 Processing helix chain 'H' and resid 478 through 482 removed outlier: 3.793A pdb=" N LYS H 481 " --> pdb=" O GLN H 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 504 Processing helix chain 'H' and resid 535 through 548 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.933A pdb=" N SER A 254 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 251 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 280 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA A 253 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 449 Processing sheet with id=AA4, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.484A pdb=" N LYS A 488 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 512 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE A 490 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLU A 514 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA A 509 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL A 533 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A 511 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.933A pdb=" N SER B 254 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 251 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL B 280 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA B 253 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 Processing sheet with id=AA7, first strand: chain 'B' and resid 423 through 425 removed outlier: 3.794A pdb=" N TYR C 518 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS C 488 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C 512 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE C 490 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLU C 514 " --> pdb=" O ILE C 490 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 423 through 425 removed outlier: 3.794A pdb=" N TYR C 518 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA C 509 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL C 533 " --> pdb=" O ALA C 509 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 511 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 445 through 449 Processing sheet with id=AB1, first strand: chain 'B' and resid 488 through 490 removed outlier: 6.770A pdb=" N ALA B 509 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL B 533 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL B 511 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 488 through 490 removed outlier: 7.822A pdb=" N THR C 424 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE B 516 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.934A pdb=" N SER C 254 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 251 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL C 280 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA C 253 " --> pdb=" O VAL C 280 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 187 through 191 Processing sheet with id=AB5, first strand: chain 'C' and resid 445 through 449 Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.934A pdb=" N SER D 254 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU D 251 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL D 280 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA D 253 " --> pdb=" O VAL D 280 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 187 through 191 Processing sheet with id=AB8, first strand: chain 'D' and resid 423 through 425 removed outlier: 3.711A pdb=" N TYR E 518 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 423 through 425 removed outlier: 3.711A pdb=" N TYR E 518 " --> pdb=" O THR D 424 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA E 509 " --> pdb=" O VAL E 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL E 533 " --> pdb=" O ALA E 509 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL E 511 " --> pdb=" O PHE E 531 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 445 through 449 Processing sheet with id=AC2, first strand: chain 'D' and resid 488 through 490 removed outlier: 6.769A pdb=" N ALA D 509 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL D 533 " --> pdb=" O ALA D 509 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL D 511 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 488 through 490 removed outlier: 7.790A pdb=" N THR E 424 " --> pdb=" O GLU D 514 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE D 516 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.934A pdb=" N SER E 254 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU E 251 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL E 280 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA E 253 " --> pdb=" O VAL E 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 187 through 191 Processing sheet with id=AC6, first strand: chain 'E' and resid 445 through 449 Processing sheet with id=AC7, first strand: chain 'F' and resid 89 through 91 removed outlier: 4.934A pdb=" N SER F 254 " --> pdb=" O ILE F 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU F 251 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL F 280 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA F 253 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 187 through 191 Processing sheet with id=AC9, first strand: chain 'F' and resid 423 through 425 removed outlier: 3.742A pdb=" N TYR G 518 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 423 through 425 removed outlier: 3.742A pdb=" N TYR G 518 " --> pdb=" O THR F 424 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA G 509 " --> pdb=" O VAL G 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL G 533 " --> pdb=" O ALA G 509 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL G 511 " --> pdb=" O PHE G 531 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 445 through 449 Processing sheet with id=AD3, first strand: chain 'F' and resid 488 through 490 removed outlier: 6.485A pdb=" N LYS F 488 " --> pdb=" O LEU F 510 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL F 512 " --> pdb=" O LYS F 488 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE F 490 " --> pdb=" O VAL F 512 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU F 514 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA F 509 " --> pdb=" O VAL F 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL F 533 " --> pdb=" O ALA F 509 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL F 511 " --> pdb=" O PHE F 531 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 488 through 490 removed outlier: 6.485A pdb=" N LYS F 488 " --> pdb=" O LEU F 510 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL F 512 " --> pdb=" O LYS F 488 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE F 490 " --> pdb=" O VAL F 512 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU F 514 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR G 424 " --> pdb=" O GLU F 514 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE F 516 " --> pdb=" O THR G 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 89 through 91 removed outlier: 4.933A pdb=" N SER G 254 " --> pdb=" O ILE G 373 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU G 251 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL G 280 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA G 253 " --> pdb=" O VAL G 280 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 187 through 191 Processing sheet with id=AD7, first strand: chain 'G' and resid 445 through 449 Processing sheet with id=AD8, first strand: chain 'H' and resid 89 through 91 removed outlier: 4.933A pdb=" N SER H 254 " --> pdb=" O ILE H 373 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU H 251 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL H 280 " --> pdb=" O LEU H 251 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA H 253 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 187 through 191 Processing sheet with id=AE1, first strand: chain 'H' and resid 445 through 449 Processing sheet with id=AE2, first strand: chain 'H' and resid 488 through 490 removed outlier: 6.484A pdb=" N LYS H 488 " --> pdb=" O LEU H 510 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL H 512 " --> pdb=" O LYS H 488 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE H 490 " --> pdb=" O VAL H 512 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLU H 514 " --> pdb=" O ILE H 490 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA H 509 " --> pdb=" O VAL H 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL H 533 " --> pdb=" O ALA H 509 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL H 511 " --> pdb=" O PHE H 531 " (cutoff:3.500A) 1376 hydrogen bonds defined for protein. 3768 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: 24.17 Time building geometry restraints manager: 15.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 31728 1.08 - 1.32: 5592 1.32 - 1.55: 26872 1.55 - 1.79: 104 1.79 - 2.03: 208 Bond restraints: 64504 Sorted by residual: bond pdb=" C4' LLP B 119 " pdb="H4'1 LLP B 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C4' LLP E 119 " pdb="H4'1 LLP E 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C4' LLP D 119 " pdb="H4'1 LLP D 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" C4' LLP H 119 " pdb="H4'1 LLP H 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" C6 LLP E 119 " pdb=" H6 LLP E 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.84e+01 ... (remaining 64499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 116579 2.86 - 5.71: 462 5.71 - 8.57: 23 8.57 - 11.42: 8 11.42 - 14.28: 8 Bond angle restraints: 117080 Sorted by residual: angle pdb=" O LLP A 119 " pdb=" C LLP A 119 " pdb=" N ASP A 120 " ideal model delta sigma weight residual 123.00 108.72 14.28 1.60e+00 3.91e-01 7.97e+01 angle pdb=" O LLP F 119 " pdb=" C LLP F 119 " pdb=" N ASP F 120 " ideal model delta sigma weight residual 123.00 108.73 14.27 1.60e+00 3.91e-01 7.95e+01 angle pdb=" O LLP E 119 " pdb=" C LLP E 119 " pdb=" N ASP E 120 " ideal model delta sigma weight residual 123.00 108.74 14.26 1.60e+00 3.91e-01 7.94e+01 angle pdb=" O LLP C 119 " pdb=" C LLP C 119 " pdb=" N ASP C 120 " ideal model delta sigma weight residual 123.00 108.75 14.25 1.60e+00 3.91e-01 7.94e+01 angle pdb=" O LLP D 119 " pdb=" C LLP D 119 " pdb=" N ASP D 120 " ideal model delta sigma weight residual 123.00 108.76 14.24 1.60e+00 3.91e-01 7.92e+01 ... (remaining 117075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 26533 17.40 - 34.79: 2292 34.79 - 52.19: 676 52.19 - 69.58: 291 69.58 - 86.98: 104 Dihedral angle restraints: 29896 sinusoidal: 16800 harmonic: 13096 Sorted by residual: dihedral pdb=" CA GLN G 528 " pdb=" C GLN G 528 " pdb=" N MET G 529 " pdb=" CA MET G 529 " ideal model delta harmonic sigma weight residual 180.00 -144.54 -35.46 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA GLN F 528 " pdb=" C GLN F 528 " pdb=" N MET F 529 " pdb=" CA MET F 529 " ideal model delta harmonic sigma weight residual -180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA GLN E 528 " pdb=" C GLN E 528 " pdb=" N MET E 529 " pdb=" CA MET E 529 " ideal model delta harmonic sigma weight residual -180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 ... (remaining 29893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3192 0.029 - 0.057: 1127 0.057 - 0.086: 268 0.086 - 0.114: 291 0.114 - 0.143: 82 Chirality restraints: 4960 Sorted by residual: chirality pdb=" CA ILE E 516 " pdb=" N ILE E 516 " pdb=" C ILE E 516 " pdb=" CB ILE E 516 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE C 516 " pdb=" N ILE C 516 " pdb=" C ILE C 516 " pdb=" CB ILE C 516 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE A 516 " pdb=" N ILE A 516 " pdb=" C ILE A 516 " pdb=" CB ILE A 516 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 4957 not shown) Planarity restraints: 9504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LLP F 119 " -0.073 2.00e-02 2.50e+03 1.35e-01 1.83e+02 pdb=" C LLP F 119 " 0.234 2.00e-02 2.50e+03 pdb=" O LLP F 119 " -0.085 2.00e-02 2.50e+03 pdb=" N ASP F 120 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP D 119 " -0.073 2.00e-02 2.50e+03 1.35e-01 1.82e+02 pdb=" C LLP D 119 " 0.234 2.00e-02 2.50e+03 pdb=" O LLP D 119 " -0.085 2.00e-02 2.50e+03 pdb=" N ASP D 120 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP A 119 " 0.073 2.00e-02 2.50e+03 1.35e-01 1.82e+02 pdb=" C LLP A 119 " -0.234 2.00e-02 2.50e+03 pdb=" O LLP A 119 " 0.085 2.00e-02 2.50e+03 pdb=" N ASP A 120 " 0.076 2.00e-02 2.50e+03 ... (remaining 9501 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 4742 2.21 - 2.81: 138196 2.81 - 3.41: 180161 3.41 - 4.00: 237694 4.00 - 4.60: 366196 Nonbonded interactions: 926989 Sorted by model distance: nonbonded pdb=" OE2 GLU E 201 " pdb=" HH TYR F 484 " model vdw 1.616 2.450 nonbonded pdb=" OE2 GLU A 201 " pdb=" HH TYR B 484 " model vdw 1.622 2.450 nonbonded pdb=" OE2 GLU H 304 " pdb=" HZ2 LYS H 384 " model vdw 1.625 2.450 nonbonded pdb=" OE2 GLU G 304 " pdb=" HZ2 LYS G 384 " model vdw 1.626 2.450 nonbonded pdb=" OE2 GLU D 304 " pdb=" HZ2 LYS D 384 " model vdw 1.626 2.450 ... (remaining 926984 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: 0.24 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 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: 0.840 Extract box with map and model: 1.980 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 103.430 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.004 0.079 32568 Z= 0.246 Angle : 0.655 14.280 44232 Z= 0.347 Chirality : 0.040 0.143 4960 Planarity : 0.006 0.135 5656 Dihedral : 14.756 86.977 12120 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.59 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.92 (0.14), residues: 4016 helix: 0.95 (0.15), residues: 1432 sheet: 0.11 (0.21), residues: 600 loop : 0.71 (0.15), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 208 HIS 0.006 0.001 HIS A 66 PHE 0.016 0.001 PHE H 531 TYR 0.029 0.002 TYR G 518 ARG 0.005 0.000 ARG E 527 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 4.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 474 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7740 (mp10) REVERT: C 126 MET cc_start: 0.8529 (mtp) cc_final: 0.8280 (mtp) REVERT: C 364 LEU cc_start: 0.6855 (mt) cc_final: 0.6461 (mt) REVERT: C 391 MET cc_start: 0.7833 (mmm) cc_final: 0.7560 (mmm) REVERT: F 126 MET cc_start: 0.8601 (mtp) cc_final: 0.8344 (mtp) REVERT: F 391 MET cc_start: 0.7851 (mmm) cc_final: 0.7609 (mmm) REVERT: G 505 MET cc_start: 0.7581 (mmt) cc_final: 0.7366 (mmp) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.9972 time to fit residues: 558.3749 Evaluate side-chains 240 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 3.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 233 optimal weight: 0.6980 chunk 363 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.119273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.094830 restraints weight = 228786.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.097469 restraints weight = 131347.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.098033 restraints weight = 85828.791| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32568 Z= 0.188 Angle : 0.556 7.534 44232 Z= 0.285 Chirality : 0.043 0.158 4960 Planarity : 0.004 0.036 5656 Dihedral : 7.893 89.265 4448 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.53 % Allowed : 11.24 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 4016 helix: 0.72 (0.14), residues: 1512 sheet: 0.22 (0.20), residues: 608 loop : 0.43 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 208 HIS 0.003 0.001 HIS A 507 PHE 0.011 0.001 PHE E 531 TYR 0.020 0.001 TYR B 518 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 259 time to evaluate : 4.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 540 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8580 (tt) REVERT: C 126 MET cc_start: 0.8317 (mtp) cc_final: 0.8069 (mtp) REVERT: D 429 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.6306 (tt) REVERT: D 540 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8432 (tt) REVERT: E 429 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6313 (tt) REVERT: E 540 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8482 (tt) REVERT: F 126 MET cc_start: 0.8282 (mtp) cc_final: 0.8035 (mtp) REVERT: F 540 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8232 (tp) REVERT: G 540 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8634 (tt) outliers start: 18 outliers final: 3 residues processed: 270 average time/residue: 0.8432 time to fit residues: 364.0368 Evaluate side-chains 224 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain H residue 241 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 313 optimal weight: 7.9990 chunk 272 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 chunk 193 optimal weight: 0.5980 chunk 213 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 340 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 513 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.115668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.091085 restraints weight = 229872.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092698 restraints weight = 139390.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.093401 restraints weight = 111939.649| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 32568 Z= 0.242 Angle : 0.550 7.549 44232 Z= 0.282 Chirality : 0.042 0.153 4960 Planarity : 0.004 0.053 5656 Dihedral : 7.802 88.605 4448 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.02 % Allowed : 11.89 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.13), residues: 4016 helix: 0.81 (0.14), residues: 1504 sheet: 0.06 (0.20), residues: 608 loop : 0.41 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 208 HIS 0.005 0.001 HIS H 507 PHE 0.010 0.001 PHE D 332 TYR 0.013 0.001 TYR B 518 ARG 0.007 0.001 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 3.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6633 (t0) REVERT: A 391 MET cc_start: 0.6923 (mmm) cc_final: 0.6481 (mtp) REVERT: B 429 ILE cc_start: 0.6272 (OUTLIER) cc_final: 0.6008 (tt) REVERT: B 540 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8555 (tt) REVERT: C 126 MET cc_start: 0.8351 (mtp) cc_final: 0.8150 (mtp) REVERT: C 391 MET cc_start: 0.7978 (mmm) cc_final: 0.7706 (mmm) REVERT: C 538 ASP cc_start: 0.7925 (m-30) cc_final: 0.7648 (m-30) REVERT: D 173 MET cc_start: 0.8522 (mmt) cc_final: 0.8154 (mmt) REVERT: D 328 ASP cc_start: 0.7631 (m-30) cc_final: 0.7296 (m-30) REVERT: D 429 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6635 (tt) REVERT: D 540 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8547 (tt) REVERT: E 171 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7603 (tm-30) REVERT: E 173 MET cc_start: 0.8494 (mmt) cc_final: 0.8130 (mmt) REVERT: E 328 ASP cc_start: 0.7658 (m-30) cc_final: 0.7323 (m-30) REVERT: E 429 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6594 (tt) REVERT: E 540 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8547 (tt) REVERT: F 126 MET cc_start: 0.8302 (mtp) cc_final: 0.8102 (mtp) REVERT: F 391 MET cc_start: 0.8010 (mmm) cc_final: 0.7752 (mmm) REVERT: F 538 ASP cc_start: 0.7880 (m-30) cc_final: 0.7625 (m-30) REVERT: F 540 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8296 (tp) REVERT: G 540 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8543 (tt) REVERT: H 129 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7128 (t0) REVERT: H 391 MET cc_start: 0.7040 (mmm) cc_final: 0.6620 (mtp) outliers start: 35 outliers final: 15 residues processed: 245 average time/residue: 0.8277 time to fit residues: 333.1556 Evaluate side-chains 218 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 328 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 341 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 320 optimal weight: 0.3980 chunk 321 optimal weight: 9.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 ASN E 294 ASN G 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.111721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086547 restraints weight = 230176.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086529 restraints weight = 137909.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.087667 restraints weight = 115288.824| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 32568 Z= 0.377 Angle : 0.610 7.093 44232 Z= 0.319 Chirality : 0.044 0.185 4960 Planarity : 0.004 0.047 5656 Dihedral : 8.073 88.106 4448 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.43 % Allowed : 12.88 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.13), residues: 4016 helix: 0.45 (0.13), residues: 1504 sheet: -0.19 (0.20), residues: 600 loop : 0.31 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 208 HIS 0.006 0.001 HIS D 67 PHE 0.021 0.002 PHE C 385 TYR 0.016 0.002 TYR F 163 ARG 0.004 0.001 ARG F 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 3.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: D 302 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: D 429 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7170 (tt) REVERT: D 540 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8655 (tt) REVERT: E 173 MET cc_start: 0.8556 (mmt) cc_final: 0.8218 (mmt) REVERT: E 302 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: E 429 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7121 (tt) REVERT: E 540 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8687 (tt) REVERT: F 302 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: F 531 PHE cc_start: 0.7209 (m-10) cc_final: 0.7003 (m-10) REVERT: F 540 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8491 (tp) REVERT: H 129 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7027 (t0) outliers start: 49 outliers final: 27 residues processed: 237 average time/residue: 0.8307 time to fit residues: 321.7590 Evaluate side-chains 225 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 502 ILE Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 362 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 323 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 ASN E 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.110116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.085122 restraints weight = 229410.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086380 restraints weight = 136656.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087220 restraints weight = 128236.246| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 32568 Z= 0.398 Angle : 0.625 6.714 44232 Z= 0.327 Chirality : 0.045 0.174 4960 Planarity : 0.005 0.048 5656 Dihedral : 8.129 89.471 4448 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.99 % Allowed : 13.73 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.13), residues: 4016 helix: 0.13 (0.13), residues: 1504 sheet: -0.40 (0.20), residues: 600 loop : 0.10 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 208 HIS 0.006 0.001 HIS F 519 PHE 0.023 0.002 PHE C 385 TYR 0.018 0.002 TYR H 163 ARG 0.005 0.001 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 191 time to evaluate : 4.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 173 MET cc_start: 0.8425 (mmt) cc_final: 0.8212 (mmt) REVERT: C 302 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: C 434 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8740 (p) REVERT: C 531 PHE cc_start: 0.7222 (m-10) cc_final: 0.6993 (m-80) REVERT: D 302 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: D 540 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8722 (tt) REVERT: E 173 MET cc_start: 0.8563 (mmt) cc_final: 0.8221 (mmt) REVERT: E 302 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: E 540 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8738 (tt) REVERT: F 302 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: F 540 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8455 (tp) REVERT: G 451 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5903 (mp0) REVERT: G 505 MET cc_start: 0.8225 (mmt) cc_final: 0.7996 (mmt) REVERT: H 129 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7086 (t0) REVERT: H 314 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8623 (p) outliers start: 68 outliers final: 36 residues processed: 243 average time/residue: 0.8054 time to fit residues: 322.0350 Evaluate side-chains 231 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 370 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 210 optimal weight: 0.0980 chunk 390 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 366 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.110621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.085547 restraints weight = 228030.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087194 restraints weight = 129896.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087926 restraints weight = 117864.221| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 32568 Z= 0.306 Angle : 0.570 6.798 44232 Z= 0.293 Chirality : 0.043 0.166 4960 Planarity : 0.004 0.044 5656 Dihedral : 7.993 89.884 4448 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.66 % Allowed : 14.28 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4016 helix: 0.29 (0.13), residues: 1504 sheet: -0.27 (0.21), residues: 560 loop : 0.09 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 208 HIS 0.005 0.001 HIS F 519 PHE 0.015 0.002 PHE D 385 TYR 0.012 0.001 TYR H 163 ARG 0.004 0.000 ARG F 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 194 time to evaluate : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6910 (t0) REVERT: A 314 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8649 (p) REVERT: C 302 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: C 314 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.9036 (p) REVERT: C 434 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8748 (p) REVERT: C 531 PHE cc_start: 0.7167 (m-10) cc_final: 0.6865 (m-80) REVERT: D 173 MET cc_start: 0.8523 (mmt) cc_final: 0.8321 (mmp) REVERT: D 302 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: D 540 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8692 (tt) REVERT: E 302 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: E 540 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8717 (tt) REVERT: F 302 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: F 314 VAL cc_start: 0.9289 (OUTLIER) cc_final: 0.9028 (p) REVERT: F 434 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8806 (p) REVERT: F 531 PHE cc_start: 0.7296 (m-10) cc_final: 0.6909 (m-80) REVERT: F 540 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8436 (tp) REVERT: G 451 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5881 (mp0) REVERT: G 505 MET cc_start: 0.8229 (mmt) cc_final: 0.7966 (mmt) REVERT: H 314 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8596 (p) outliers start: 57 outliers final: 36 residues processed: 238 average time/residue: 0.8103 time to fit residues: 319.3466 Evaluate side-chains 239 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 3.9990 chunk 319 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 370 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.110786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085945 restraints weight = 228128.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087234 restraints weight = 132265.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087967 restraints weight = 124225.541| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 32568 Z= 0.280 Angle : 0.556 6.540 44232 Z= 0.284 Chirality : 0.043 0.163 4960 Planarity : 0.004 0.042 5656 Dihedral : 7.907 89.508 4448 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.61 % Allowed : 14.63 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 4016 helix: 0.41 (0.14), residues: 1504 sheet: -0.23 (0.22), residues: 560 loop : 0.14 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 208 HIS 0.005 0.001 HIS F 519 PHE 0.013 0.001 PHE C 332 TYR 0.011 0.001 TYR H 163 ARG 0.004 0.000 ARG F 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 192 time to evaluate : 4.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8673 (p) REVERT: C 302 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: C 314 VAL cc_start: 0.9266 (OUTLIER) cc_final: 0.8994 (p) REVERT: C 531 PHE cc_start: 0.7217 (m-10) cc_final: 0.6891 (m-80) REVERT: D 173 MET cc_start: 0.8541 (mmt) cc_final: 0.8318 (mmp) REVERT: D 302 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: D 328 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7437 (p0) REVERT: D 540 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8649 (tt) REVERT: E 173 MET cc_start: 0.8335 (mmt) cc_final: 0.8112 (mmt) REVERT: E 302 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: E 328 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7473 (p0) REVERT: E 540 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8673 (tt) REVERT: F 302 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: F 434 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8795 (p) REVERT: F 531 PHE cc_start: 0.7266 (m-10) cc_final: 0.6942 (m-80) REVERT: F 540 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8409 (tp) REVERT: G 451 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5772 (mp0) REVERT: G 505 MET cc_start: 0.8150 (mmt) cc_final: 0.7928 (mmt) REVERT: H 314 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8577 (p) outliers start: 55 outliers final: 36 residues processed: 239 average time/residue: 0.8125 time to fit residues: 320.7659 Evaluate side-chains 238 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 3.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 277 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 228 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 348 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.112652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.087951 restraints weight = 227791.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089485 restraints weight = 130448.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090194 restraints weight = 121525.799| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32568 Z= 0.180 Angle : 0.516 6.510 44232 Z= 0.257 Chirality : 0.042 0.148 4960 Planarity : 0.004 0.040 5656 Dihedral : 7.725 88.890 4448 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.17 % Allowed : 15.16 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 4016 helix: 0.70 (0.14), residues: 1504 sheet: -0.11 (0.22), residues: 560 loop : 0.34 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 408 HIS 0.004 0.001 HIS F 519 PHE 0.013 0.001 PHE C 334 TYR 0.009 0.001 TYR D 518 ARG 0.003 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 4.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: C 314 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.9000 (p) REVERT: C 434 THR cc_start: 0.8996 (m) cc_final: 0.8761 (p) REVERT: C 531 PHE cc_start: 0.7050 (m-10) cc_final: 0.6710 (m-80) REVERT: D 173 MET cc_start: 0.8559 (mmt) cc_final: 0.8321 (mmp) REVERT: D 302 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: D 328 ASP cc_start: 0.8077 (m-30) cc_final: 0.7312 (p0) REVERT: D 540 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8607 (tt) REVERT: E 302 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: E 540 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8637 (tt) REVERT: F 302 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: F 314 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.8977 (p) REVERT: F 531 PHE cc_start: 0.7284 (m-10) cc_final: 0.6922 (m-80) REVERT: F 540 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8301 (tp) REVERT: G 505 MET cc_start: 0.8188 (mmt) cc_final: 0.7906 (mmt) outliers start: 40 outliers final: 28 residues processed: 248 average time/residue: 0.8182 time to fit residues: 334.5645 Evaluate side-chains 234 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 4.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 328 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 357 optimal weight: 6.9990 chunk 270 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 386 optimal weight: 7.9990 chunk 327 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.111829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086849 restraints weight = 227550.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088745 restraints weight = 126877.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.089481 restraints weight = 110724.243| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32568 Z= 0.234 Angle : 0.531 5.908 44232 Z= 0.267 Chirality : 0.042 0.153 4960 Planarity : 0.004 0.044 5656 Dihedral : 7.765 88.764 4448 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.43 % Allowed : 15.07 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 4016 helix: 0.72 (0.14), residues: 1504 sheet: -0.03 (0.22), residues: 552 loop : 0.33 (0.15), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 208 HIS 0.004 0.001 HIS F 519 PHE 0.012 0.001 PHE D 385 TYR 0.009 0.001 TYR A 163 ARG 0.011 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6858 (t0) REVERT: A 314 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8715 (p) REVERT: C 302 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: C 434 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8745 (p) REVERT: C 531 PHE cc_start: 0.7184 (m-10) cc_final: 0.6818 (m-80) REVERT: D 302 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: D 328 ASP cc_start: 0.8086 (m-30) cc_final: 0.7452 (p0) REVERT: D 391 MET cc_start: 0.7900 (mmt) cc_final: 0.7601 (mmt) REVERT: D 540 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8629 (tt) REVERT: E 216 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7580 (t0) REVERT: E 302 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: E 328 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7384 (p0) REVERT: F 302 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: F 314 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.8990 (p) REVERT: F 434 THR cc_start: 0.9085 (m) cc_final: 0.8824 (p) REVERT: F 531 PHE cc_start: 0.7265 (m-10) cc_final: 0.6920 (m-80) REVERT: F 540 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8457 (tp) REVERT: G 451 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.5636 (mp0) REVERT: G 505 MET cc_start: 0.8203 (mmt) cc_final: 0.7955 (mmt) outliers start: 49 outliers final: 31 residues processed: 241 average time/residue: 0.8266 time to fit residues: 330.9059 Evaluate side-chains 237 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 328 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 155 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 323 optimal weight: 9.9990 chunk 348 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 395 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 209 optimal weight: 8.9990 chunk 332 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 GLN ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 528 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.111741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.086630 restraints weight = 228739.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088750 restraints weight = 124468.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.089431 restraints weight = 108516.202| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 32568 Z= 0.275 Angle : 0.639 59.135 44232 Z= 0.353 Chirality : 0.042 0.319 4960 Planarity : 0.004 0.040 5656 Dihedral : 7.766 88.723 4448 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.29 % Allowed : 15.22 % Favored : 83.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 4016 helix: 0.71 (0.14), residues: 1504 sheet: -0.03 (0.22), residues: 552 loop : 0.33 (0.15), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 208 HIS 0.004 0.001 HIS D 203 PHE 0.013 0.001 PHE D 385 TYR 0.009 0.001 TYR A 163 ARG 0.006 0.000 ARG C 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 4.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.6859 (t0) REVERT: A 314 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8774 (p) REVERT: C 302 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: C 434 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8755 (p) REVERT: C 531 PHE cc_start: 0.7197 (m-10) cc_final: 0.6815 (m-80) REVERT: D 302 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: D 328 ASP cc_start: 0.8095 (m-30) cc_final: 0.7455 (p0) REVERT: D 540 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8635 (tt) REVERT: E 302 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: E 328 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7379 (p0) REVERT: F 302 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: F 314 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9003 (p) REVERT: F 434 THR cc_start: 0.9092 (m) cc_final: 0.8831 (p) REVERT: F 531 PHE cc_start: 0.7275 (m-10) cc_final: 0.6930 (m-80) REVERT: F 540 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8468 (tp) REVERT: G 451 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.5643 (mp0) REVERT: G 505 MET cc_start: 0.8219 (mmt) cc_final: 0.7962 (mmt) outliers start: 44 outliers final: 31 residues processed: 231 average time/residue: 0.7840 time to fit residues: 300.9798 Evaluate side-chains 235 residues out of total 3424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 431 CYS Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 328 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 214 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 50 optimal weight: 20.0000 chunk 252 optimal weight: 8.9990 chunk 264 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 395 optimal weight: 3.9990 chunk 369 optimal weight: 7.9990 chunk 379 optimal weight: 3.9990 chunk 332 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 489 GLN ** G 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.111683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.086646 restraints weight = 227775.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088639 restraints weight = 123823.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.089390 restraints weight = 108455.716| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 32568 Z= 0.275 Angle : 0.639 59.198 44232 Z= 0.352 Chirality : 0.042 0.315 4960 Planarity : 0.004 0.040 5656 Dihedral : 7.766 88.723 4448 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.26 % Allowed : 15.19 % Favored : 83.56 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 4016 helix: 0.71 (0.14), residues: 1504 sheet: -0.03 (0.22), residues: 552 loop : 0.33 (0.15), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 208 HIS 0.004 0.001 HIS D 203 PHE 0.013 0.001 PHE D 385 TYR 0.009 0.001 TYR A 163 ARG 0.006 0.000 ARG C 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11797.32 seconds wall clock time: 205 minutes 15.45 seconds (12315.45 seconds total)