Starting phenix.real_space_refine on Fri May 23 23:26:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yeh_39195/05_2025/8yeh_39195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yeh_39195/05_2025/8yeh_39195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yeh_39195/05_2025/8yeh_39195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yeh_39195/05_2025/8yeh_39195.map" model { file = "/net/cci-nas-00/data/ceres_data/8yeh_39195/05_2025/8yeh_39195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yeh_39195/05_2025/8yeh_39195.cif" } resolution = 2.86 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= 0.001 sd= 0.189 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 15985 2.51 5 N 4240 2.21 5 O 4830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25195 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "B" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "F" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3280 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 25, 'TRANS': 390} Chain breaks: 1 Restraints were copied for chains: M, L, O, N, C, E, D, G, I, H, K, J Time building chain proxies: 9.39, per 1000 atoms: 0.37 Number of scatterers: 25195 At special positions: 0 Unit cell: (141.44, 141.44, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 4830 8.00 N 4240 7.00 C 15985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.54 Conformation dependent library (CDL) restraints added in 3.1 seconds 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5930 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 45 sheets defined 12.9% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 53 through 56 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.013A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.045A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 28 removed outlier: 4.448A pdb=" N TYR F 27 " --> pdb=" O SER F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 214 removed outlier: 3.520A pdb=" N GLN F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 239 Processing helix chain 'F' and resid 280 through 284 removed outlier: 3.558A pdb=" N THR F 283 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA F 284 " --> pdb=" O GLY F 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 280 through 284' Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 384 through 395 Processing helix chain 'F' and resid 396 through 402 removed outlier: 3.714A pdb=" N GLU F 400 " --> pdb=" O SER F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 461 removed outlier: 3.552A pdb=" N GLN F 461 " --> pdb=" O ASP F 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 458 through 461' Processing helix chain 'F' and resid 462 through 472 removed outlier: 3.500A pdb=" N LYS F 467 " --> pdb=" O PRO F 463 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 472 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.013A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.045A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 28 removed outlier: 4.447A pdb=" N TYR L 27 " --> pdb=" O SER L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 214 removed outlier: 3.521A pdb=" N GLN L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 239 Processing helix chain 'L' and resid 280 through 284 removed outlier: 3.558A pdb=" N THR L 283 " --> pdb=" O SER L 280 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA L 284 " --> pdb=" O GLY L 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 280 through 284' Processing helix chain 'L' and resid 303 through 305 No H-bonds generated for 'chain 'L' and resid 303 through 305' Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 384 through 395 Processing helix chain 'L' and resid 396 through 402 removed outlier: 3.714A pdb=" N GLU L 400 " --> pdb=" O SER L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 458 through 461 removed outlier: 3.552A pdb=" N GLN L 461 " --> pdb=" O ASP L 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 458 through 461' Processing helix chain 'L' and resid 462 through 472 removed outlier: 3.501A pdb=" N LYS L 467 " --> pdb=" O PRO L 463 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA L 472 " --> pdb=" O PHE L 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.013A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.045A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 28 removed outlier: 4.448A pdb=" N TYR M 27 " --> pdb=" O SER M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 209 through 214 removed outlier: 3.520A pdb=" N GLN M 214 " --> pdb=" O PHE M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 239 Processing helix chain 'M' and resid 280 through 284 removed outlier: 3.557A pdb=" N THR M 283 " --> pdb=" O SER M 280 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA M 284 " --> pdb=" O GLY M 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 280 through 284' Processing helix chain 'M' and resid 303 through 305 No H-bonds generated for 'chain 'M' and resid 303 through 305' Processing helix chain 'M' and resid 356 through 358 No H-bonds generated for 'chain 'M' and resid 356 through 358' Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 396 through 402 removed outlier: 3.713A pdb=" N GLU M 400 " --> pdb=" O SER M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 458 through 461 removed outlier: 3.551A pdb=" N GLN M 461 " --> pdb=" O ASP M 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 458 through 461' Processing helix chain 'M' and resid 462 through 472 removed outlier: 3.500A pdb=" N LYS M 467 " --> pdb=" O PRO M 463 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA M 472 " --> pdb=" O PHE M 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.012A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.044A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 28 removed outlier: 4.448A pdb=" N TYR N 27 " --> pdb=" O SER N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 209 through 214 removed outlier: 3.520A pdb=" N GLN N 214 " --> pdb=" O PHE N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 239 Processing helix chain 'N' and resid 280 through 284 removed outlier: 3.557A pdb=" N THR N 283 " --> pdb=" O SER N 280 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA N 284 " --> pdb=" O GLY N 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 280 through 284' Processing helix chain 'N' and resid 303 through 305 No H-bonds generated for 'chain 'N' and resid 303 through 305' Processing helix chain 'N' and resid 356 through 358 No H-bonds generated for 'chain 'N' and resid 356 through 358' Processing helix chain 'N' and resid 384 through 395 Processing helix chain 'N' and resid 396 through 402 removed outlier: 3.714A pdb=" N GLU N 400 " --> pdb=" O SER N 396 " (cutoff:3.500A) Processing helix chain 'N' and resid 458 through 461 removed outlier: 3.553A pdb=" N GLN N 461 " --> pdb=" O ASP N 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 458 through 461' Processing helix chain 'N' and resid 462 through 472 removed outlier: 3.500A pdb=" N LYS N 467 " --> pdb=" O PRO N 463 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA N 472 " --> pdb=" O PHE N 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 56 Processing helix chain 'G' and resid 61 through 65 Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.013A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.045A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 28 removed outlier: 4.448A pdb=" N TYR O 27 " --> pdb=" O SER O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 209 through 214 removed outlier: 3.521A pdb=" N GLN O 214 " --> pdb=" O PHE O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 239 Processing helix chain 'O' and resid 280 through 284 removed outlier: 3.557A pdb=" N THR O 283 " --> pdb=" O SER O 280 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA O 284 " --> pdb=" O GLY O 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 280 through 284' Processing helix chain 'O' and resid 303 through 305 No H-bonds generated for 'chain 'O' and resid 303 through 305' Processing helix chain 'O' and resid 356 through 358 No H-bonds generated for 'chain 'O' and resid 356 through 358' Processing helix chain 'O' and resid 384 through 395 Processing helix chain 'O' and resid 396 through 402 removed outlier: 3.713A pdb=" N GLU O 400 " --> pdb=" O SER O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 458 through 461 removed outlier: 3.553A pdb=" N GLN O 461 " --> pdb=" O ASP O 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 458 through 461' Processing helix chain 'O' and resid 462 through 472 removed outlier: 3.500A pdb=" N LYS O 467 " --> pdb=" O PRO O 463 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA O 472 " --> pdb=" O PHE O 468 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 10 through 12 current: chain 'A' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 57 through 59 current: chain 'A' and resid 111 through 112 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.543A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 10 through 13 current: chain 'B' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 53 through 54 current: chain 'B' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'F' and resid 29 through 38 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 29 through 38 current: chain 'F' and resid 311 through 312 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 311 through 312 current: chain 'F' and resid 360 through 382 removed outlier: 6.805A pdb=" N PHE F 360 " --> pdb=" O ALA L 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 6.692A pdb=" N ILE F 52 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 71 through 76 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 71 through 76 current: chain 'F' and resid 248 through 261 removed outlier: 6.454A pdb=" N THR F 294 " --> pdb=" O ARG F 258 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU F 260 " --> pdb=" O PHE F 292 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE F 292 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 118 through 123 removed outlier: 5.104A pdb=" N GLY F 119 " --> pdb=" O MET F 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET F 149 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE F 147 " --> pdb=" O PRO F 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 188 through 194 removed outlier: 5.678A pdb=" N TRP F 169 " --> pdb=" O CYS F 229 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N CYS F 229 " --> pdb=" O TRP F 169 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET F 200 " --> pdb=" O LYS F 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 266 through 267 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 266 through 267 current: chain 'O' and resid 311 through 312 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 311 through 312 current: chain 'O' and resid 360 through 382 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 300 through 301 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 300 through 301 current: chain 'L' and resid 248 through 261 removed outlier: 6.454A pdb=" N THR L 294 " --> pdb=" O ARG L 258 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU L 260 " --> pdb=" O PHE L 292 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE L 292 " --> pdb=" O LEU L 260 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 12 current: chain 'C' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 111 through 112 Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.543A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 13 current: chain 'H' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 53 through 54 current: chain 'H' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'L' and resid 29 through 38 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 29 through 38 current: chain 'L' and resid 311 through 312 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 311 through 312 current: chain 'L' and resid 360 through 382 removed outlier: 6.813A pdb=" N PHE L 360 " --> pdb=" O ALA M 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.691A pdb=" N ILE L 52 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 118 through 123 removed outlier: 5.103A pdb=" N GLY L 119 " --> pdb=" O MET L 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET L 149 " --> pdb=" O GLY L 119 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE L 147 " --> pdb=" O PRO L 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 188 through 194 removed outlier: 5.678A pdb=" N TRP L 169 " --> pdb=" O CYS L 229 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N CYS L 229 " --> pdb=" O TRP L 169 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET L 200 " --> pdb=" O LYS L 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 300 through 301 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 300 through 301 current: chain 'M' and resid 248 through 261 removed outlier: 6.454A pdb=" N THR M 294 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU M 260 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE M 292 " --> pdb=" O LEU M 260 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 12 current: chain 'D' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 59 current: chain 'D' and resid 111 through 112 Processing sheet with id=AC5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.543A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 13 current: chain 'I' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 53 through 54 current: chain 'I' and resid 97 through 98 Processing sheet with id=AC7, first strand: chain 'M' and resid 29 through 38 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 29 through 38 current: chain 'M' and resid 311 through 312 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 311 through 312 current: chain 'M' and resid 360 through 382 removed outlier: 6.832A pdb=" N PHE M 360 " --> pdb=" O ALA N 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 52 through 53 removed outlier: 6.692A pdb=" N ILE M 52 " --> pdb=" O LEU M 61 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 118 through 123 removed outlier: 5.103A pdb=" N GLY M 119 " --> pdb=" O MET M 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET M 149 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE M 147 " --> pdb=" O PRO M 121 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 188 through 194 removed outlier: 5.677A pdb=" N TRP M 169 " --> pdb=" O CYS M 229 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N CYS M 229 " --> pdb=" O TRP M 169 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET M 200 " --> pdb=" O LYS M 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 300 through 301 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 300 through 301 current: chain 'N' and resid 248 through 261 removed outlier: 6.454A pdb=" N THR N 294 " --> pdb=" O ARG N 258 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU N 260 " --> pdb=" O PHE N 292 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE N 292 " --> pdb=" O LEU N 260 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 12 current: chain 'E' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 59 current: chain 'E' and resid 111 through 112 Processing sheet with id=AD5, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.542A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 13 current: chain 'J' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 53 through 54 current: chain 'J' and resid 97 through 98 Processing sheet with id=AD7, first strand: chain 'N' and resid 29 through 38 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 29 through 38 current: chain 'N' and resid 311 through 312 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 311 through 312 current: chain 'N' and resid 360 through 382 removed outlier: 6.795A pdb=" N PHE N 360 " --> pdb=" O ALA O 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'N' and resid 52 through 53 removed outlier: 6.692A pdb=" N ILE N 52 " --> pdb=" O LEU N 61 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 118 through 123 removed outlier: 5.104A pdb=" N GLY N 119 " --> pdb=" O MET N 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET N 149 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE N 147 " --> pdb=" O PRO N 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 188 through 194 removed outlier: 5.678A pdb=" N TRP N 169 " --> pdb=" O CYS N 229 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N CYS N 229 " --> pdb=" O TRP N 169 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET N 200 " --> pdb=" O LYS N 230 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 300 through 301 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 300 through 301 current: chain 'O' and resid 248 through 261 removed outlier: 6.454A pdb=" N THR O 294 " --> pdb=" O ARG O 258 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU O 260 " --> pdb=" O PHE O 292 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE O 292 " --> pdb=" O LEU O 260 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 111 through 112 Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.542A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 13 current: chain 'K' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 53 through 54 current: chain 'K' and resid 97 through 98 Processing sheet with id=AE7, first strand: chain 'O' and resid 52 through 53 removed outlier: 6.693A pdb=" N ILE O 52 " --> pdb=" O LEU O 61 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 118 through 123 removed outlier: 5.103A pdb=" N GLY O 119 " --> pdb=" O MET O 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET O 149 " --> pdb=" O GLY O 119 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE O 147 " --> pdb=" O PRO O 121 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 188 through 194 removed outlier: 5.678A pdb=" N TRP O 169 " --> pdb=" O CYS O 229 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N CYS O 229 " --> pdb=" O TRP O 169 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET O 200 " --> pdb=" O LYS O 230 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 945 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: 7.17 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8140 1.34 - 1.46: 6064 1.46 - 1.58: 11406 1.58 - 1.69: 0 1.69 - 1.81: 205 Bond restraints: 25815 Sorted by residual: bond pdb=" CB PRO L 182 " pdb=" CG PRO L 182 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.65e-01 bond pdb=" CB PRO O 182 " pdb=" CG PRO O 182 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.52e-01 bond pdb=" CB PRO F 182 " pdb=" CG PRO F 182 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.47e-01 bond pdb=" CB PRO M 182 " pdb=" CG PRO M 182 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.44e-01 bond pdb=" CB PRO N 182 " pdb=" CG PRO N 182 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.37e-01 ... (remaining 25810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 33841 1.32 - 2.64: 970 2.64 - 3.97: 229 3.97 - 5.29: 20 5.29 - 6.61: 10 Bond angle restraints: 35070 Sorted by residual: angle pdb=" C GLY O 110 " pdb=" N GLN O 111 " pdb=" CA GLN O 111 " ideal model delta sigma weight residual 121.80 127.22 -5.42 2.44e+00 1.68e-01 4.93e+00 angle pdb=" C GLY F 110 " pdb=" N GLN F 111 " pdb=" CA GLN F 111 " ideal model delta sigma weight residual 121.80 127.20 -5.40 2.44e+00 1.68e-01 4.90e+00 angle pdb=" C GLY L 110 " pdb=" N GLN L 111 " pdb=" CA GLN L 111 " ideal model delta sigma weight residual 121.80 127.18 -5.38 2.44e+00 1.68e-01 4.87e+00 angle pdb=" C GLY N 110 " pdb=" N GLN N 111 " pdb=" CA GLN N 111 " ideal model delta sigma weight residual 121.80 127.17 -5.37 2.44e+00 1.68e-01 4.85e+00 angle pdb=" C GLY M 110 " pdb=" N GLN M 111 " pdb=" CA GLN M 111 " ideal model delta sigma weight residual 121.80 127.16 -5.36 2.44e+00 1.68e-01 4.83e+00 ... (remaining 35065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 14065 17.56 - 35.13: 1015 35.13 - 52.69: 145 52.69 - 70.25: 30 70.25 - 87.81: 20 Dihedral angle restraints: 15275 sinusoidal: 5980 harmonic: 9295 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 153.97 -60.97 1 1.00e+01 1.00e-02 4.94e+01 dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 153.96 -60.96 1 1.00e+01 1.00e-02 4.94e+01 dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual 93.00 153.96 -60.96 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 15272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2145 0.029 - 0.058: 1034 0.058 - 0.086: 300 0.086 - 0.115: 267 0.115 - 0.144: 89 Chirality restraints: 3835 Sorted by residual: chirality pdb=" CA VAL G 37 " pdb=" N VAL G 37 " pdb=" C VAL G 37 " pdb=" CB VAL G 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE J 48 " pdb=" N ILE J 48 " pdb=" C ILE J 48 " pdb=" CB ILE J 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE H 48 " pdb=" N ILE H 48 " pdb=" C ILE H 48 " pdb=" CB ILE H 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 3832 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 181 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO O 182 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO O 182 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 182 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN N 181 " -0.064 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO N 182 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO N 182 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO N 182 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 181 " -0.064 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO F 182 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO F 182 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO F 182 " -0.052 5.00e-02 4.00e+02 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2798 2.75 - 3.29: 21023 3.29 - 3.83: 39457 3.83 - 4.36: 49973 4.36 - 4.90: 88817 Nonbonded interactions: 202068 Sorted by model distance: nonbonded pdb=" O ILE O 306 " pdb=" OH TYR O 311 " model vdw 2.218 3.040 nonbonded pdb=" O ILE N 306 " pdb=" OH TYR N 311 " model vdw 2.219 3.040 nonbonded pdb=" O ILE F 306 " pdb=" OH TYR F 311 " model vdw 2.219 3.040 nonbonded pdb=" O ILE M 306 " pdb=" OH TYR M 311 " model vdw 2.220 3.040 nonbonded pdb=" O ILE L 306 " pdb=" OH TYR L 311 " model vdw 2.220 3.040 ... (remaining 202063 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: 0.19 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 46.720 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0003 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25825 Z= 0.131 Angle : 0.555 6.612 35090 Z= 0.290 Chirality : 0.046 0.144 3835 Planarity : 0.006 0.096 4530 Dihedral : 12.536 87.814 9315 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.15), residues: 3185 helix: 1.04 (0.39), residues: 165 sheet: 0.43 (0.15), residues: 1240 loop : -0.58 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 36 HIS 0.005 0.001 HIS L 120 PHE 0.031 0.002 PHE N 455 TYR 0.015 0.001 TYR C 32 ARG 0.008 0.001 ARG J 24 Details of bonding type rmsd hydrogen bonds : bond 0.14258 ( 370) hydrogen bonds : angle 5.41583 ( 945) SS BOND : bond 0.00585 ( 10) SS BOND : angle 1.13967 ( 20) covalent geometry : bond 0.00306 (25815) covalent geometry : angle 0.55490 (35070) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 191 ILE cc_start: 0.1027 (mt) cc_final: 0.0726 (mt) REVERT: C 48 MET cc_start: 0.0646 (mtp) cc_final: -0.0854 (ppp) REVERT: N 212 THR cc_start: 0.1671 (p) cc_final: 0.1316 (t) REVERT: N 214 GLN cc_start: 0.3781 (mt0) cc_final: 0.2996 (mt0) REVERT: G 117 LEU cc_start: 0.3235 (tp) cc_final: 0.2927 (pt) REVERT: O 74 ARG cc_start: 0.1935 (ttt180) cc_final: 0.1620 (ttt180) REVERT: O 151 TYR cc_start: 0.2264 (m-10) cc_final: 0.1001 (m-80) REVERT: O 342 MET cc_start: 0.2164 (mtm) cc_final: 0.1111 (pp-130) outliers start: 0 outliers final: 1 residues processed: 152 average time/residue: 1.1383 time to fit residues: 206.8484 Evaluate side-chains 122 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 30.0000 chunk 238 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 286 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN A 6 GLN F 96 GLN F 120 HIS ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 GLN F 320 ASN L 192 ASN L 305 GLN D 1 GLN I 38 HIS M 155 GLN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 254 GLN ** M 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 373 GLN E 6 GLN E 30 ASN J 38 HIS ** N 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 ASN ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 155 GLN ** N 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 ASN O 192 ASN O 328 GLN O 359 ASN O 373 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.315237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.299759 restraints weight = 31692.030| |-----------------------------------------------------------------------------| r_work (start): 0.4968 rms_B_bonded: 1.53 r_work: 0.4871 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1120 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 25825 Z= 0.255 Angle : 0.861 14.239 35090 Z= 0.449 Chirality : 0.056 0.374 3835 Planarity : 0.007 0.078 4530 Dihedral : 5.757 70.309 3498 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.47 % Allowed : 7.12 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.79 (0.14), residues: 3185 helix: -0.16 (0.35), residues: 170 sheet: 0.16 (0.16), residues: 1080 loop : -0.97 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 36 HIS 0.017 0.003 HIS M 120 PHE 0.043 0.004 PHE M 374 TYR 0.037 0.004 TYR L 291 ARG 0.010 0.001 ARG C 100 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 370) hydrogen bonds : angle 6.02346 ( 945) SS BOND : bond 0.00615 ( 10) SS BOND : angle 1.84147 ( 20) covalent geometry : bond 0.00567 (25815) covalent geometry : angle 0.85980 (35070) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.3761 (t-100) cc_final: 0.2968 (t-100) REVERT: F 191 ILE cc_start: 0.3672 (OUTLIER) cc_final: 0.3442 (mt) REVERT: F 388 MET cc_start: 0.0373 (mmp) cc_final: -0.1629 (tmt) REVERT: F 394 MET cc_start: 0.0432 (ttp) cc_final: 0.0230 (ttp) REVERT: L 314 GLN cc_start: -0.0486 (pt0) cc_final: -0.1008 (pt0) REVERT: L 394 MET cc_start: 0.2530 (ptm) cc_final: 0.0202 (ttp) REVERT: M 200 MET cc_start: -0.0252 (mmm) cc_final: -0.1591 (tpt) REVERT: M 299 MET cc_start: 0.2204 (mtm) cc_final: 0.1225 (ptm) REVERT: J 4 MET cc_start: -0.1539 (mtp) cc_final: -0.1884 (mtt) REVERT: N 35 TYR cc_start: 0.3869 (m-80) cc_final: 0.3281 (m-80) REVERT: N 299 MET cc_start: 0.3450 (tmm) cc_final: 0.2954 (ttt) REVERT: G 81 MET cc_start: 0.1719 (tpt) cc_final: 0.0403 (tpt) REVERT: G 108 LEU cc_start: 0.1885 (OUTLIER) cc_final: 0.0218 (tp) REVERT: O 74 ARG cc_start: 0.4533 (ttt180) cc_final: 0.3614 (ttt-90) REVERT: O 299 MET cc_start: 0.1415 (mtp) cc_final: 0.0823 (mpt) outliers start: 41 outliers final: 22 residues processed: 153 average time/residue: 1.0830 time to fit residues: 200.1198 Evaluate side-chains 134 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 342 MET Chi-restraints excluded: chain L residue 364 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 208 MET Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain O residue 388 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 280 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 304 optimal weight: 0.1980 chunk 149 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 305 GLN F 317 GLN F 320 ASN ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 153 GLN D 6 GLN M 254 GLN M 305 GLN J 76 ASN N 96 GLN ** N 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 359 ASN K 38 HIS O 96 GLN ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.318430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.303197 restraints weight = 31306.619| |-----------------------------------------------------------------------------| r_work (start): 0.5007 rms_B_bonded: 1.68 r_work: 0.4917 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.4917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1106 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25825 Z= 0.112 Angle : 0.540 13.384 35090 Z= 0.278 Chirality : 0.045 0.169 3835 Planarity : 0.005 0.065 4530 Dihedral : 4.518 22.760 3495 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.51 % Allowed : 9.35 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.69 (0.14), residues: 3185 helix: 0.13 (0.36), residues: 170 sheet: -0.05 (0.16), residues: 1140 loop : -0.75 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 106 HIS 0.007 0.001 HIS O 120 PHE 0.017 0.002 PHE O 73 TYR 0.016 0.001 TYR N 91 ARG 0.004 0.001 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 370) hydrogen bonds : angle 5.28633 ( 945) SS BOND : bond 0.00263 ( 10) SS BOND : angle 0.77539 ( 20) covalent geometry : bond 0.00251 (25815) covalent geometry : angle 0.53952 (35070) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 189 GLU cc_start: 0.1709 (OUTLIER) cc_final: 0.1042 (tt0) REVERT: F 191 ILE cc_start: 0.3537 (mt) cc_final: 0.3161 (mp) REVERT: F 328 GLN cc_start: 0.4776 (mm-40) cc_final: 0.3583 (tt0) REVERT: F 388 MET cc_start: 0.1264 (mmp) cc_final: -0.1103 (tmt) REVERT: L 314 GLN cc_start: -0.0428 (pt0) cc_final: -0.0676 (pt0) REVERT: L 330 PHE cc_start: 0.1040 (m-80) cc_final: 0.0830 (m-80) REVERT: M 200 MET cc_start: -0.0504 (mmm) cc_final: -0.1494 (tpt) REVERT: J 4 MET cc_start: -0.1348 (mtp) cc_final: -0.1566 (mtp) REVERT: N 35 TYR cc_start: 0.3432 (m-80) cc_final: 0.2791 (m-80) REVERT: N 299 MET cc_start: 0.2760 (tmm) cc_final: 0.2523 (tpp) REVERT: N 394 MET cc_start: -0.0254 (OUTLIER) cc_final: -0.1126 (ptt) REVERT: G 81 MET cc_start: 0.2188 (tpt) cc_final: 0.1303 (tpt) REVERT: O 74 ARG cc_start: 0.5279 (ttt180) cc_final: 0.4195 (ttt-90) outliers start: 42 outliers final: 20 residues processed: 133 average time/residue: 1.1478 time to fit residues: 182.8645 Evaluate side-chains 123 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 277 ILE Chi-restraints excluded: chain L residue 299 MET Chi-restraints excluded: chain L residue 342 MET Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 149 MET Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 336 THR Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 394 MET Chi-restraints excluded: chain O residue 331 VAL Chi-restraints excluded: chain O residue 388 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 264 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 269 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 257 optimal weight: 0.6980 chunk 209 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN F 76 HIS F 96 GLN F 143 ASN ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN F 320 ASN F 327 ASN ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 ASN L 314 GLN D 62 GLN I 34 ASN I 55 GLN I 89 GLN ** M 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 ASN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 341 ASN E 30 ASN J 6 GLN N 76 HIS N 192 ASN ** N 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 308 ASN N 328 GLN O 96 GLN ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 216 ASN O 254 GLN ** O 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 373 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5201 r_free = 0.5201 target = 0.328713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.317777 restraints weight = 32068.282| |-----------------------------------------------------------------------------| r_work (start): 0.5118 rms_B_bonded: 1.29 r_work: 0.5058 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4985 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2032 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 25825 Z= 0.327 Angle : 1.095 19.992 35090 Z= 0.569 Chirality : 0.062 0.410 3835 Planarity : 0.009 0.119 4530 Dihedral : 7.522 40.143 3495 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.23 % Favored : 91.68 % Rotamer: Outliers : 3.96 % Allowed : 12.48 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.14), residues: 3185 helix: -0.51 (0.38), residues: 160 sheet: -0.97 (0.16), residues: 1070 loop : -1.66 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP F 100 HIS 0.019 0.004 HIS F 120 PHE 0.048 0.005 PHE F 210 TYR 0.038 0.005 TYR J 92 ARG 0.015 0.002 ARG N 71 Details of bonding type rmsd hydrogen bonds : bond 0.05474 ( 370) hydrogen bonds : angle 7.53913 ( 945) SS BOND : bond 0.00809 ( 10) SS BOND : angle 1.62851 ( 20) covalent geometry : bond 0.00716 (25815) covalent geometry : angle 1.09414 (35070) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 140 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.4446 (OUTLIER) cc_final: 0.4146 (mm-40) REVERT: B 95 ARG cc_start: 0.5575 (ttm170) cc_final: 0.5069 (mtt90) REVERT: F 149 MET cc_start: 0.0378 (pmm) cc_final: 0.0168 (pmm) REVERT: F 151 TYR cc_start: 0.1866 (OUTLIER) cc_final: -0.0002 (m-10) REVERT: F 189 GLU cc_start: 0.3290 (OUTLIER) cc_final: 0.2529 (pt0) REVERT: F 202 ASP cc_start: 0.2359 (OUTLIER) cc_final: 0.1662 (m-30) REVERT: F 237 MET cc_start: 0.1799 (OUTLIER) cc_final: 0.1490 (ttp) REVERT: F 328 GLN cc_start: 0.5101 (mm-40) cc_final: 0.4481 (tt0) REVERT: F 342 MET cc_start: 0.5378 (mpt) cc_final: 0.4618 (mpt) REVERT: F 388 MET cc_start: 0.1663 (mmp) cc_final: -0.1426 (tmt) REVERT: C 48 MET cc_start: 0.3176 (mtp) cc_final: 0.2914 (mtp) REVERT: H 87 TYR cc_start: 0.3617 (m-80) cc_final: 0.3219 (m-80) REVERT: L 117 ILE cc_start: -0.0872 (OUTLIER) cc_final: -0.1532 (mp) REVERT: L 277 ILE cc_start: 0.1066 (OUTLIER) cc_final: 0.0635 (mt) REVERT: L 314 GLN cc_start: 0.0250 (pt0) cc_final: -0.1230 (mt0) REVERT: L 394 MET cc_start: 0.2014 (ptt) cc_final: 0.1222 (ttp) REVERT: D 32 TYR cc_start: 0.1277 (OUTLIER) cc_final: 0.0453 (t80) REVERT: I 36 TYR cc_start: 0.2709 (m-80) cc_final: 0.1135 (m-80) REVERT: M 25 ASP cc_start: 0.1724 (m-30) cc_final: 0.1247 (p0) REVERT: M 70 TYR cc_start: 0.1841 (m-80) cc_final: 0.1479 (m-80) REVERT: M 115 VAL cc_start: -0.0436 (OUTLIER) cc_final: -0.0831 (m) REVERT: M 135 TYR cc_start: 0.4224 (OUTLIER) cc_final: 0.3151 (t80) REVERT: M 200 MET cc_start: -0.0033 (mmm) cc_final: -0.1359 (mmm) REVERT: M 394 MET cc_start: -0.2470 (mtt) cc_final: -0.3179 (ptt) REVERT: M 471 GLN cc_start: 0.4871 (OUTLIER) cc_final: 0.1441 (mm-40) REVERT: J 4 MET cc_start: -0.0594 (mtp) cc_final: -0.0862 (mtt) REVERT: J 83 PHE cc_start: 0.0503 (OUTLIER) cc_final: 0.0118 (p90) REVERT: N 30 ARG cc_start: 0.1679 (mtt180) cc_final: -0.0066 (ptp90) REVERT: N 149 MET cc_start: 0.3354 (ptp) cc_final: 0.3120 (ptp) REVERT: N 253 GLU cc_start: 0.2372 (OUTLIER) cc_final: 0.1437 (mt-10) REVERT: N 394 MET cc_start: -0.1893 (OUTLIER) cc_final: -0.2174 (ptt) REVERT: N 454 LYS cc_start: 0.3502 (tmtt) cc_final: 0.3194 (mptt) REVERT: G 81 MET cc_start: 0.2642 (tpt) cc_final: 0.0541 (ppp) REVERT: G 108 LEU cc_start: 0.2111 (OUTLIER) cc_final: 0.1281 (tp) REVERT: K 4 MET cc_start: 0.1325 (OUTLIER) cc_final: -0.2350 (ttm) REVERT: O 49 TYR cc_start: 0.3672 (OUTLIER) cc_final: 0.2740 (m-10) REVERT: O 342 MET cc_start: 0.0017 (mtm) cc_final: -0.0265 (pp-130) REVERT: O 355 TYR cc_start: 0.3001 (t80) cc_final: 0.1094 (t80) REVERT: O 452 LYS cc_start: 0.2929 (mttm) cc_final: 0.2667 (tptm) outliers start: 110 outliers final: 47 residues processed: 222 average time/residue: 1.0190 time to fit residues: 273.6580 Evaluate side-chains 190 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 76 HIS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 225 CYS Chi-restraints excluded: chain L residue 277 ILE Chi-restraints excluded: chain L residue 296 SER Chi-restraints excluded: chain L residue 311 TYR Chi-restraints excluded: chain L residue 364 LEU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 55 GLN Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 471 GLN Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain N residue 47 HIS Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 237 MET Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 301 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 394 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 208 MET Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 319 HIS Chi-restraints excluded: chain O residue 327 ASN Chi-restraints excluded: chain O residue 331 VAL Chi-restraints excluded: chain O residue 374 PHE Chi-restraints excluded: chain O residue 388 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 115 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 18 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 HIS ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN L 153 GLN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 ASN I 89 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 254 GLN N 254 GLN N 327 ASN O 153 GLN O 254 GLN ** O 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.327731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.316527 restraints weight = 32033.687| |-----------------------------------------------------------------------------| r_work (start): 0.5113 rms_B_bonded: 1.28 r_work: 0.5050 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4976 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1796 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25825 Z= 0.126 Angle : 0.623 10.067 35090 Z= 0.325 Chirality : 0.047 0.192 3835 Planarity : 0.005 0.064 4530 Dihedral : 5.609 26.928 3495 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.12 % Allowed : 15.11 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 3185 helix: -0.15 (0.38), residues: 170 sheet: -0.68 (0.17), residues: 1020 loop : -1.46 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 106 HIS 0.012 0.002 HIS F 76 PHE 0.020 0.002 PHE J 83 TYR 0.023 0.002 TYR O 49 ARG 0.012 0.001 ARG I 95 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 370) hydrogen bonds : angle 6.13884 ( 945) SS BOND : bond 0.00276 ( 10) SS BOND : angle 1.34787 ( 20) covalent geometry : bond 0.00280 (25815) covalent geometry : angle 0.62250 (35070) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 123 time to evaluate : 2.369 Fit side-chains REVERT: A 64 PHE cc_start: 0.1414 (m-10) cc_final: 0.0668 (m-10) REVERT: B 95 ARG cc_start: 0.5377 (OUTLIER) cc_final: 0.4397 (mtp180) REVERT: F 149 MET cc_start: 0.0002 (pmm) cc_final: -0.0828 (tmt) REVERT: F 169 TRP cc_start: 0.3365 (m100) cc_final: 0.3154 (m100) REVERT: F 189 GLU cc_start: 0.2959 (OUTLIER) cc_final: 0.0072 (tp30) REVERT: F 237 MET cc_start: 0.1946 (OUTLIER) cc_final: 0.1493 (ttp) REVERT: F 342 MET cc_start: 0.5163 (mpt) cc_final: 0.4127 (mpt) REVERT: F 388 MET cc_start: 0.1884 (mmp) cc_final: -0.1284 (tmt) REVERT: C 63 ARG cc_start: 0.4195 (ptt-90) cc_final: 0.3399 (ptt90) REVERT: L 252 ARG cc_start: 0.7498 (ptm160) cc_final: 0.6820 (ptp-110) REVERT: L 299 MET cc_start: 0.4342 (OUTLIER) cc_final: 0.3584 (tpt) REVERT: L 314 GLN cc_start: 0.0106 (OUTLIER) cc_final: -0.1536 (tt0) REVERT: L 394 MET cc_start: 0.1778 (ptt) cc_final: 0.0206 (ttp) REVERT: L 455 PHE cc_start: -0.0355 (OUTLIER) cc_final: -0.1005 (m-80) REVERT: I 28 MET cc_start: 0.3761 (OUTLIER) cc_final: 0.3326 (mpm) REVERT: I 36 TYR cc_start: 0.2307 (m-80) cc_final: 0.1150 (m-80) REVERT: M 135 TYR cc_start: 0.4168 (OUTLIER) cc_final: 0.3433 (t80) REVERT: M 200 MET cc_start: -0.0286 (mmm) cc_final: -0.1464 (mmm) REVERT: J 83 PHE cc_start: 0.0468 (OUTLIER) cc_final: 0.0034 (p90) REVERT: N 30 ARG cc_start: 0.1540 (mtt180) cc_final: -0.0123 (ptp90) REVERT: N 149 MET cc_start: 0.2942 (ptp) cc_final: 0.1892 (ptm) REVERT: N 394 MET cc_start: -0.1439 (OUTLIER) cc_final: -0.1797 (ptt) REVERT: N 454 LYS cc_start: 0.2885 (tmtt) cc_final: 0.2512 (mppt) REVERT: G 81 MET cc_start: 0.2655 (tpt) cc_final: 0.2282 (tpt) REVERT: K 4 MET cc_start: 0.1286 (pmm) cc_final: -0.2266 (ttm) REVERT: O 74 ARG cc_start: 0.6244 (ttt180) cc_final: 0.5212 (mmm-85) REVERT: O 342 MET cc_start: -0.0289 (mtm) cc_final: -0.0764 (pp-130) REVERT: O 452 LYS cc_start: 0.3157 (mttm) cc_final: 0.2911 (tptm) outliers start: 59 outliers final: 27 residues processed: 164 average time/residue: 1.0999 time to fit residues: 216.9627 Evaluate side-chains 159 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 299 MET Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 336 THR Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain N residue 47 HIS Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 237 MET Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 394 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 319 HIS Chi-restraints excluded: chain O residue 331 VAL Chi-restraints excluded: chain O residue 388 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 287 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 107 optimal weight: 0.2980 chunk 284 optimal weight: 0.9980 chunk 239 optimal weight: 0.0870 chunk 219 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 GLN C 6 GLN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN M 96 GLN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN G 30 ASN ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.330020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5121 r_free = 0.5121 target = 0.318778 restraints weight = 31783.963| |-----------------------------------------------------------------------------| r_work (start): 0.5116 rms_B_bonded: 1.28 r_work: 0.5052 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4978 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1744 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25825 Z= 0.102 Angle : 0.546 12.289 35090 Z= 0.282 Chirality : 0.045 0.173 3835 Planarity : 0.005 0.057 4530 Dihedral : 4.852 22.149 3495 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.23 % Allowed : 15.72 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 3185 helix: 0.30 (0.39), residues: 170 sheet: -0.49 (0.16), residues: 1055 loop : -1.26 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 47 HIS 0.005 0.001 HIS N 47 PHE 0.028 0.002 PHE M 261 TYR 0.025 0.001 TYR M 390 ARG 0.009 0.000 ARG I 95 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 370) hydrogen bonds : angle 5.60878 ( 945) SS BOND : bond 0.00433 ( 10) SS BOND : angle 0.87198 ( 20) covalent geometry : bond 0.00227 (25815) covalent geometry : angle 0.54596 (35070) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 123 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.1170 (m-10) cc_final: 0.0872 (m-10) REVERT: A 90 ASP cc_start: 0.0534 (OUTLIER) cc_final: 0.0218 (t70) REVERT: B 95 ARG cc_start: 0.5510 (ttm170) cc_final: 0.4551 (mtp180) REVERT: F 47 HIS cc_start: 0.2990 (OUTLIER) cc_final: 0.2205 (m170) REVERT: F 149 MET cc_start: 0.0209 (pmm) cc_final: -0.0809 (tmt) REVERT: F 237 MET cc_start: 0.1346 (OUTLIER) cc_final: 0.0980 (ttp) REVERT: F 342 MET cc_start: 0.5310 (mpt) cc_final: 0.4201 (mpt) REVERT: F 388 MET cc_start: 0.1402 (mmp) cc_final: -0.1556 (tmt) REVERT: C 63 ARG cc_start: 0.4175 (ptt-90) cc_final: 0.3425 (ptt90) REVERT: H 94 THR cc_start: 0.0774 (OUTLIER) cc_final: -0.1236 (t) REVERT: L 299 MET cc_start: 0.4225 (OUTLIER) cc_final: 0.3014 (ttm) REVERT: L 314 GLN cc_start: 0.0294 (OUTLIER) cc_final: -0.0478 (pt0) REVERT: L 394 MET cc_start: 0.2353 (ptt) cc_final: 0.0513 (ttp) REVERT: L 455 PHE cc_start: -0.0170 (OUTLIER) cc_final: -0.0851 (m-80) REVERT: I 28 MET cc_start: 0.3955 (OUTLIER) cc_final: 0.3347 (mpm) REVERT: I 36 TYR cc_start: 0.2322 (m-80) cc_final: 0.1100 (m-80) REVERT: M 200 MET cc_start: -0.0227 (mmm) cc_final: -0.1416 (mmm) REVERT: J 4 MET cc_start: 0.2005 (ttm) cc_final: 0.1675 (ttp) REVERT: J 83 PHE cc_start: 0.0484 (OUTLIER) cc_final: 0.0059 (p90) REVERT: N 30 ARG cc_start: 0.1282 (mtt180) cc_final: -0.0296 (ptp90) REVERT: N 96 GLN cc_start: 0.4890 (mm110) cc_final: 0.4347 (mt0) REVERT: N 111 GLN cc_start: 0.3025 (mm-40) cc_final: 0.1427 (tm-30) REVERT: N 149 MET cc_start: 0.3018 (ptp) cc_final: 0.2309 (ptm) REVERT: N 394 MET cc_start: -0.1353 (OUTLIER) cc_final: -0.1699 (ptt) REVERT: G 81 MET cc_start: 0.2517 (tpt) cc_final: -0.0142 (ppp) REVERT: K 4 MET cc_start: 0.1312 (pmm) cc_final: -0.2185 (mpp) REVERT: O 74 ARG cc_start: 0.6259 (ttt180) cc_final: 0.5037 (mmm-85) REVERT: O 342 MET cc_start: -0.0318 (mtm) cc_final: -0.0771 (pp-130) REVERT: O 452 LYS cc_start: 0.3125 (mttm) cc_final: 0.2830 (tptm) outliers start: 62 outliers final: 33 residues processed: 170 average time/residue: 1.1288 time to fit residues: 229.5274 Evaluate side-chains 164 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 299 MET Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain N residue 47 HIS Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 237 MET Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 394 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 319 HIS Chi-restraints excluded: chain O residue 331 VAL Chi-restraints excluded: chain O residue 455 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 40.0000 chunk 92 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 254 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 GLN C 6 GLN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5222 r_free = 0.5222 target = 0.331411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.320555 restraints weight = 31744.222| |-----------------------------------------------------------------------------| r_work (start): 0.5133 rms_B_bonded: 1.30 r_work: 0.5063 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4984 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1962 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25825 Z= 0.142 Angle : 0.636 13.693 35090 Z= 0.327 Chirality : 0.047 0.202 3835 Planarity : 0.005 0.055 4530 Dihedral : 5.208 23.180 3495 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.55 % Allowed : 16.04 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 3185 helix: 0.42 (0.39), residues: 170 sheet: -0.68 (0.17), residues: 1035 loop : -1.30 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 100 HIS 0.014 0.002 HIS M 259 PHE 0.037 0.002 PHE M 261 TYR 0.022 0.002 TYR O 49 ARG 0.008 0.001 ARG N 71 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 370) hydrogen bonds : angle 5.84905 ( 945) SS BOND : bond 0.00516 ( 10) SS BOND : angle 0.90508 ( 20) covalent geometry : bond 0.00320 (25815) covalent geometry : angle 0.63550 (35070) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 130 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.1174 (m-10) cc_final: 0.0627 (m-10) REVERT: B 95 ARG cc_start: 0.5646 (OUTLIER) cc_final: 0.4870 (mtm180) REVERT: F 47 HIS cc_start: 0.3307 (OUTLIER) cc_final: 0.2439 (m170) REVERT: F 149 MET cc_start: -0.0019 (pmm) cc_final: -0.1123 (tmt) REVERT: F 237 MET cc_start: 0.2014 (ttp) cc_final: 0.1799 (ttt) REVERT: F 342 MET cc_start: 0.5372 (mpt) cc_final: 0.4203 (mpt) REVERT: C 63 ARG cc_start: 0.4108 (ptt-90) cc_final: 0.3282 (ptt-90) REVERT: H 94 THR cc_start: 0.1070 (OUTLIER) cc_final: -0.1240 (t) REVERT: L 150 ASP cc_start: 0.3371 (OUTLIER) cc_final: 0.0085 (t0) REVERT: L 299 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4374 (tmm) REVERT: L 314 GLN cc_start: -0.0193 (OUTLIER) cc_final: -0.1566 (tt0) REVERT: L 455 PHE cc_start: 0.0238 (OUTLIER) cc_final: -0.0388 (m-80) REVERT: I 11 LEU cc_start: -0.2456 (OUTLIER) cc_final: -0.2894 (mp) REVERT: I 36 TYR cc_start: 0.2764 (m-80) cc_final: 0.1320 (m-80) REVERT: M 135 TYR cc_start: 0.4183 (OUTLIER) cc_final: 0.3391 (t80) REVERT: M 200 MET cc_start: -0.0103 (mmm) cc_final: -0.1483 (mmm) REVERT: M 251 ARG cc_start: 0.1309 (OUTLIER) cc_final: -0.0152 (ttm-80) REVERT: M 299 MET cc_start: 0.1309 (OUTLIER) cc_final: 0.0880 (ttm) REVERT: E 36 TRP cc_start: 0.4601 (m100) cc_final: 0.3580 (m100) REVERT: J 4 MET cc_start: 0.2502 (ttm) cc_final: 0.2180 (ttp) REVERT: J 83 PHE cc_start: 0.0444 (OUTLIER) cc_final: -0.0110 (p90) REVERT: N 30 ARG cc_start: 0.1448 (mtt180) cc_final: -0.0107 (ptp90) REVERT: N 375 ILE cc_start: 0.2186 (OUTLIER) cc_final: 0.1713 (mm) REVERT: N 454 LYS cc_start: 0.5079 (ttpp) cc_final: 0.4000 (mppt) REVERT: G 81 MET cc_start: 0.3180 (tpt) cc_final: 0.0066 (ppp) REVERT: K 28 MET cc_start: 0.2916 (mpp) cc_final: 0.2097 (mpp) REVERT: O 74 ARG cc_start: 0.6533 (ttt180) cc_final: 0.5128 (ttt180) REVERT: O 342 MET cc_start: -0.0162 (mtm) cc_final: -0.0649 (pp-130) REVERT: O 452 LYS cc_start: 0.3138 (mttm) cc_final: 0.2792 (tptm) outliers start: 71 outliers final: 39 residues processed: 181 average time/residue: 1.2247 time to fit residues: 265.1024 Evaluate side-chains 179 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 127 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 249 TYR Chi-restraints excluded: chain L residue 299 MET Chi-restraints excluded: chain L residue 311 TYR Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 299 MET Chi-restraints excluded: chain M residue 336 THR Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain N residue 47 HIS Chi-restraints excluded: chain N residue 237 MET Chi-restraints excluded: chain N residue 288 SER Chi-restraints excluded: chain N residue 306 ILE Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 319 HIS Chi-restraints excluded: chain O residue 331 VAL Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 388 MET Chi-restraints excluded: chain O residue 455 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 11 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 159 optimal weight: 4.9990 chunk 299 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 GLN ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 HIS F 373 GLN H 38 HIS ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 143 ASN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5228 r_free = 0.5228 target = 0.332272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.321317 restraints weight = 31709.948| |-----------------------------------------------------------------------------| r_work (start): 0.5136 rms_B_bonded: 1.31 r_work: 0.5064 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4986 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1858 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25825 Z= 0.101 Angle : 0.544 14.953 35090 Z= 0.278 Chirality : 0.045 0.183 3835 Planarity : 0.004 0.053 4530 Dihedral : 4.695 22.313 3495 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.19 % Allowed : 16.62 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3185 helix: 0.61 (0.39), residues: 170 sheet: -0.58 (0.16), residues: 1070 loop : -1.17 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 106 HIS 0.005 0.001 HIS N 47 PHE 0.018 0.002 PHE J 83 TYR 0.018 0.001 TYR O 49 ARG 0.007 0.000 ARG I 95 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 370) hydrogen bonds : angle 5.49995 ( 945) SS BOND : bond 0.00388 ( 10) SS BOND : angle 1.02867 ( 20) covalent geometry : bond 0.00227 (25815) covalent geometry : angle 0.54403 (35070) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 125 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.5489 (OUTLIER) cc_final: 0.4539 (mtp180) REVERT: F 149 MET cc_start: -0.0073 (pmm) cc_final: -0.1291 (tmt) REVERT: F 151 TYR cc_start: 0.1704 (OUTLIER) cc_final: -0.0365 (m-10) REVERT: F 189 GLU cc_start: 0.3185 (OUTLIER) cc_final: 0.0602 (tp30) REVERT: F 342 MET cc_start: 0.5543 (mpt) cc_final: 0.4438 (mpt) REVERT: F 388 MET cc_start: 0.0659 (mmp) cc_final: -0.2213 (tmt) REVERT: C 63 ARG cc_start: 0.4153 (ptt-90) cc_final: 0.3220 (ptt-90) REVERT: L 299 MET cc_start: 0.5289 (OUTLIER) cc_final: 0.4647 (ttm) REVERT: L 314 GLN cc_start: -0.0050 (OUTLIER) cc_final: -0.0416 (pt0) REVERT: L 394 MET cc_start: 0.2997 (ptt) cc_final: 0.0921 (ttp) REVERT: L 455 PHE cc_start: 0.0090 (OUTLIER) cc_final: -0.0359 (m-80) REVERT: I 11 LEU cc_start: -0.2493 (OUTLIER) cc_final: -0.2891 (mp) REVERT: I 28 MET cc_start: 0.4329 (OUTLIER) cc_final: 0.3667 (mpm) REVERT: I 36 TYR cc_start: 0.2720 (m-80) cc_final: 0.1296 (m-80) REVERT: M 25 ASP cc_start: 0.1316 (m-30) cc_final: 0.1001 (p0) REVERT: M 75 ILE cc_start: -0.1786 (OUTLIER) cc_final: -0.2408 (mm) REVERT: M 135 TYR cc_start: 0.4029 (OUTLIER) cc_final: 0.3269 (t80) REVERT: M 200 MET cc_start: -0.0073 (mmm) cc_final: -0.1105 (ppp) REVERT: M 251 ARG cc_start: 0.1112 (OUTLIER) cc_final: -0.0004 (ttm-80) REVERT: M 299 MET cc_start: 0.1705 (OUTLIER) cc_final: 0.1233 (ttm) REVERT: E 36 TRP cc_start: 0.4405 (m100) cc_final: 0.3247 (m100) REVERT: J 83 PHE cc_start: 0.0431 (OUTLIER) cc_final: -0.0127 (p90) REVERT: N 30 ARG cc_start: 0.1298 (mtt180) cc_final: -0.0316 (ptp90) REVERT: N 129 THR cc_start: 0.3348 (OUTLIER) cc_final: 0.2478 (p) REVERT: N 149 MET cc_start: 0.2711 (ptp) cc_final: 0.2012 (ptm) REVERT: N 375 ILE cc_start: 0.2046 (OUTLIER) cc_final: 0.1588 (mm) REVERT: N 394 MET cc_start: -0.0293 (ppp) cc_final: -0.0954 (tpt) REVERT: N 455 PHE cc_start: 0.4002 (OUTLIER) cc_final: 0.2797 (m-80) REVERT: G 81 MET cc_start: 0.3186 (tpt) cc_final: -0.0122 (ppp) REVERT: G 108 LEU cc_start: 0.2173 (OUTLIER) cc_final: 0.0203 (tp) REVERT: K 4 MET cc_start: 0.1114 (pmm) cc_final: -0.2254 (mpp) REVERT: K 28 MET cc_start: 0.2691 (mpp) cc_final: 0.1889 (mpp) REVERT: O 74 ARG cc_start: 0.6334 (ttt180) cc_final: 0.4948 (ttp-170) REVERT: O 219 GLU cc_start: 0.2665 (OUTLIER) cc_final: 0.0345 (mm-30) REVERT: O 342 MET cc_start: -0.0310 (mtm) cc_final: -0.0764 (pp-130) REVERT: O 452 LYS cc_start: 0.3209 (mttm) cc_final: 0.2894 (tptm) outliers start: 61 outliers final: 36 residues processed: 171 average time/residue: 1.1444 time to fit residues: 235.6736 Evaluate side-chains 176 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 122 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain L residue 299 MET Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 149 MET Chi-restraints excluded: chain M residue 248 PHE Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 299 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain N residue 47 HIS Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 237 MET Chi-restraints excluded: chain N residue 288 SER Chi-restraints excluded: chain N residue 306 ILE Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 455 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 219 GLU Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 319 HIS Chi-restraints excluded: chain O residue 331 VAL Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 455 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 121 optimal weight: 7.9990 chunk 246 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 186 optimal weight: 0.1980 chunk 299 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 ASN ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 ASN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 285 ASN ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5231 r_free = 0.5231 target = 0.333127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.322545 restraints weight = 31992.541| |-----------------------------------------------------------------------------| r_work (start): 0.5152 rms_B_bonded: 1.32 r_work: 0.5083 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.5004 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.5004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2051 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25825 Z= 0.142 Angle : 0.639 14.995 35090 Z= 0.326 Chirality : 0.047 0.212 3835 Planarity : 0.005 0.057 4530 Dihedral : 5.130 24.221 3495 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.59 % Allowed : 16.51 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.15), residues: 3185 helix: 0.51 (0.39), residues: 170 sheet: -0.48 (0.17), residues: 975 loop : -1.38 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 100 HIS 0.010 0.002 HIS N 120 PHE 0.019 0.002 PHE E 55 TYR 0.023 0.002 TYR O 49 ARG 0.019 0.001 ARG I 95 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 370) hydrogen bonds : angle 5.83183 ( 945) SS BOND : bond 0.00485 ( 10) SS BOND : angle 1.11354 ( 20) covalent geometry : bond 0.00318 (25815) covalent geometry : angle 0.63855 (35070) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 132 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.5672 (OUTLIER) cc_final: 0.4911 (mtt90) REVERT: F 47 HIS cc_start: 0.3540 (OUTLIER) cc_final: 0.2361 (m170) REVERT: F 76 HIS cc_start: 0.4827 (m90) cc_final: 0.4452 (m90) REVERT: F 149 MET cc_start: 0.0380 (pmm) cc_final: -0.1043 (tmt) REVERT: F 169 TRP cc_start: 0.3865 (m100) cc_final: 0.3307 (m100) REVERT: F 189 GLU cc_start: 0.3352 (OUTLIER) cc_final: 0.2519 (pt0) REVERT: F 253 GLU cc_start: 0.4967 (OUTLIER) cc_final: 0.3765 (mt-10) REVERT: F 342 MET cc_start: 0.5436 (mpt) cc_final: 0.4148 (mpt) REVERT: C 63 ARG cc_start: 0.4555 (ptt-90) cc_final: 0.3920 (ptt-90) REVERT: H 28 MET cc_start: 0.2917 (mmt) cc_final: 0.2025 (pp-130) REVERT: H 87 TYR cc_start: 0.3722 (m-80) cc_final: 0.3481 (m-80) REVERT: L 299 MET cc_start: 0.5247 (OUTLIER) cc_final: 0.4651 (tmm) REVERT: L 314 GLN cc_start: -0.0162 (OUTLIER) cc_final: -0.1444 (tt0) REVERT: I 11 LEU cc_start: -0.2304 (OUTLIER) cc_final: -0.2639 (mp) REVERT: I 36 TYR cc_start: 0.2857 (m-80) cc_final: 0.1405 (m-80) REVERT: M 25 ASP cc_start: 0.1166 (m-30) cc_final: 0.0901 (p0) REVERT: M 135 TYR cc_start: 0.4154 (OUTLIER) cc_final: 0.3265 (t80) REVERT: M 200 MET cc_start: 0.0285 (mmm) cc_final: -0.0615 (ppp) REVERT: M 299 MET cc_start: 0.2099 (OUTLIER) cc_final: 0.1714 (ttm) REVERT: M 394 MET cc_start: -0.0803 (OUTLIER) cc_final: -0.1143 (mtt) REVERT: E 36 TRP cc_start: 0.4474 (m100) cc_final: 0.2850 (m100) REVERT: E 48 MET cc_start: 0.1739 (tpp) cc_final: 0.1400 (tmt) REVERT: E 81 MET cc_start: -0.0582 (OUTLIER) cc_final: -0.0916 (tmm) REVERT: J 83 PHE cc_start: 0.0698 (OUTLIER) cc_final: -0.0028 (p90) REVERT: N 30 ARG cc_start: 0.1676 (mtt180) cc_final: 0.0489 (ptt-90) REVERT: N 253 GLU cc_start: 0.3043 (OUTLIER) cc_final: 0.2329 (mt-10) REVERT: N 342 MET cc_start: 0.1825 (OUTLIER) cc_final: 0.0786 (ttp) REVERT: N 375 ILE cc_start: 0.2507 (OUTLIER) cc_final: 0.2030 (mm) REVERT: N 394 MET cc_start: -0.0819 (ppp) cc_final: -0.2044 (mtm) REVERT: G 81 MET cc_start: 0.3671 (tpt) cc_final: 0.0842 (tmm) REVERT: G 108 LEU cc_start: 0.2104 (OUTLIER) cc_final: 0.0673 (tp) REVERT: K 28 MET cc_start: 0.2973 (mpp) cc_final: 0.2331 (mpp) REVERT: O 49 TYR cc_start: 0.3633 (OUTLIER) cc_final: 0.3141 (m-10) REVERT: O 74 ARG cc_start: 0.6581 (ttt180) cc_final: 0.6048 (ttt180) REVERT: O 120 HIS cc_start: 0.4683 (OUTLIER) cc_final: 0.3306 (t-170) REVERT: O 188 LEU cc_start: 0.0028 (OUTLIER) cc_final: -0.0622 (mp) REVERT: O 219 GLU cc_start: 0.3049 (OUTLIER) cc_final: 0.0831 (mm-30) REVERT: O 342 MET cc_start: -0.0232 (mtm) cc_final: -0.0730 (pp-130) REVERT: O 452 LYS cc_start: 0.3101 (mttm) cc_final: 0.2834 (tptm) outliers start: 72 outliers final: 41 residues processed: 183 average time/residue: 1.1009 time to fit residues: 241.4901 Evaluate side-chains 189 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 128 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 252 ARG Chi-restraints excluded: chain L residue 299 MET Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain M residue 47 HIS Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 283 THR Chi-restraints excluded: chain M residue 299 MET Chi-restraints excluded: chain M residue 336 THR Chi-restraints excluded: chain M residue 394 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain N residue 47 HIS Chi-restraints excluded: chain N residue 237 MET Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 288 SER Chi-restraints excluded: chain N residue 306 ILE Chi-restraints excluded: chain N residue 342 MET Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 455 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 120 HIS Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 219 GLU Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 319 HIS Chi-restraints excluded: chain O residue 327 ASN Chi-restraints excluded: chain O residue 331 VAL Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 142 optimal weight: 0.0470 chunk 289 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 245 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 285 optimal weight: 0.7980 chunk 251 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 319 HIS ** 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 = 0.5216 r_free = 0.5216 target = 0.332765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.321193 restraints weight = 32130.224| |-----------------------------------------------------------------------------| r_work (start): 0.5113 rms_B_bonded: 1.45 r_work: 0.5056 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4978 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1895 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25825 Z= 0.094 Angle : 0.533 16.174 35090 Z= 0.272 Chirality : 0.044 0.185 3835 Planarity : 0.004 0.054 4530 Dihedral : 4.586 22.068 3495 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.91 % Allowed : 17.30 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 3185 helix: 0.79 (0.40), residues: 170 sheet: -0.50 (0.17), residues: 1065 loop : -1.19 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 47 HIS 0.005 0.001 HIS N 120 PHE 0.018 0.001 PHE J 83 TYR 0.015 0.001 TYR O 49 ARG 0.007 0.000 ARG I 95 Details of bonding type rmsd hydrogen bonds : bond 0.02664 ( 370) hydrogen bonds : angle 5.41690 ( 945) SS BOND : bond 0.00358 ( 10) SS BOND : angle 0.95459 ( 20) covalent geometry : bond 0.00211 (25815) covalent geometry : angle 0.53238 (35070) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.5572 (OUTLIER) cc_final: 0.4485 (mtp180) REVERT: F 47 HIS cc_start: 0.3521 (OUTLIER) cc_final: 0.2409 (m170) REVERT: F 76 HIS cc_start: 0.4613 (m90) cc_final: 0.4247 (m90) REVERT: F 169 TRP cc_start: 0.3484 (m100) cc_final: 0.3091 (m100) REVERT: F 189 GLU cc_start: 0.2929 (OUTLIER) cc_final: 0.2352 (pt0) REVERT: F 237 MET cc_start: 0.0561 (tmm) cc_final: -0.0131 (tmm) REVERT: F 253 GLU cc_start: 0.4884 (OUTLIER) cc_final: 0.3826 (mt-10) REVERT: F 342 MET cc_start: 0.5561 (mpt) cc_final: 0.4450 (mpt) REVERT: C 63 ARG cc_start: 0.4538 (ptt-90) cc_final: 0.3688 (ptt-90) REVERT: H 28 MET cc_start: 0.3020 (mmt) cc_final: 0.2155 (pp-130) REVERT: L 299 MET cc_start: 0.5335 (OUTLIER) cc_final: 0.5040 (ttt) REVERT: L 314 GLN cc_start: 0.0570 (OUTLIER) cc_final: 0.0146 (pt0) REVERT: L 330 PHE cc_start: 0.4983 (m-80) cc_final: 0.3715 (m-80) REVERT: L 394 MET cc_start: 0.2906 (ptt) cc_final: 0.0644 (ttp) REVERT: D 48 MET cc_start: 0.3844 (tpp) cc_final: 0.2882 (ttt) REVERT: D 69 THR cc_start: 0.1364 (OUTLIER) cc_final: 0.1023 (m) REVERT: I 11 LEU cc_start: -0.2553 (OUTLIER) cc_final: -0.2810 (mp) REVERT: I 28 MET cc_start: 0.4442 (OUTLIER) cc_final: 0.3677 (mpm) REVERT: I 36 TYR cc_start: 0.2964 (m-80) cc_final: 0.1594 (m-80) REVERT: M 25 ASP cc_start: 0.1163 (m-30) cc_final: 0.0847 (p0) REVERT: M 135 TYR cc_start: 0.3951 (OUTLIER) cc_final: 0.3066 (t80) REVERT: M 200 MET cc_start: 0.0437 (mmm) cc_final: -0.0613 (ppp) REVERT: M 251 ARG cc_start: 0.0986 (OUTLIER) cc_final: 0.0088 (ttm-80) REVERT: M 299 MET cc_start: 0.1660 (OUTLIER) cc_final: 0.0438 (tmm) REVERT: M 394 MET cc_start: -0.0910 (OUTLIER) cc_final: -0.1424 (mtt) REVERT: E 36 TRP cc_start: 0.4364 (m100) cc_final: 0.2845 (m100) REVERT: E 81 MET cc_start: -0.0803 (tmm) cc_final: -0.1085 (tmm) REVERT: J 83 PHE cc_start: 0.0690 (OUTLIER) cc_final: 0.0156 (p90) REVERT: N 129 THR cc_start: 0.3980 (OUTLIER) cc_final: 0.3084 (p) REVERT: N 375 ILE cc_start: 0.2152 (OUTLIER) cc_final: 0.1655 (mm) REVERT: N 394 MET cc_start: -0.0476 (ppp) cc_final: -0.1283 (tpt) REVERT: G 108 LEU cc_start: 0.1999 (OUTLIER) cc_final: 0.0106 (tp) REVERT: K 4 MET cc_start: 0.1207 (OUTLIER) cc_final: -0.2125 (mpp) REVERT: K 28 MET cc_start: 0.2870 (mpp) cc_final: 0.2061 (mpp) REVERT: O 74 ARG cc_start: 0.6376 (ttt180) cc_final: 0.6063 (ttt180) REVERT: O 120 HIS cc_start: 0.4335 (OUTLIER) cc_final: 0.2815 (t-170) REVERT: O 188 LEU cc_start: 0.0158 (OUTLIER) cc_final: -0.0395 (mp) REVERT: O 219 GLU cc_start: 0.2667 (OUTLIER) cc_final: 0.0706 (mm-30) REVERT: O 342 MET cc_start: -0.0222 (mtm) cc_final: -0.0634 (pp-130) REVERT: O 452 LYS cc_start: 0.3187 (mttm) cc_final: 0.2888 (tptm) outliers start: 53 outliers final: 28 residues processed: 163 average time/residue: 1.0666 time to fit residues: 209.4131 Evaluate side-chains 174 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 252 ARG Chi-restraints excluded: chain L residue 299 MET Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 283 THR Chi-restraints excluded: chain M residue 299 MET Chi-restraints excluded: chain M residue 394 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 237 MET Chi-restraints excluded: chain N residue 288 SER Chi-restraints excluded: chain N residue 306 ILE Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 455 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 120 HIS Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 219 GLU Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 331 VAL Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 64 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 212 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 214 optimal weight: 0.0370 chunk 134 optimal weight: 8.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5220 r_free = 0.5220 target = 0.333298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.321955 restraints weight = 32032.559| |-----------------------------------------------------------------------------| r_work (start): 0.5119 rms_B_bonded: 1.43 r_work: 0.5060 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4983 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1955 moved from start: 0.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25825 Z= 0.105 Angle : 0.553 16.163 35090 Z= 0.280 Chirality : 0.045 0.166 3835 Planarity : 0.005 0.055 4530 Dihedral : 4.591 20.767 3495 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.16 % Allowed : 17.30 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3185 helix: 0.95 (0.41), residues: 165 sheet: -0.63 (0.16), residues: 1095 loop : -1.11 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 47 HIS 0.006 0.001 HIS N 120 PHE 0.018 0.002 PHE J 83 TYR 0.013 0.001 TYR L 249 ARG 0.005 0.000 ARG I 95 Details of bonding type rmsd hydrogen bonds : bond 0.02754 ( 370) hydrogen bonds : angle 5.45445 ( 945) SS BOND : bond 0.00390 ( 10) SS BOND : angle 1.00747 ( 20) covalent geometry : bond 0.00238 (25815) covalent geometry : angle 0.55220 (35070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13702.51 seconds wall clock time: 237 minutes 43.81 seconds (14263.81 seconds total)