Starting phenix.real_space_refine on Sat Jun 21 11:24:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yeh_39195/06_2025/8yeh_39195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yeh_39195/06_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_39195/06_2025/8yeh_39195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yeh_39195/06_2025/8yeh_39195.map" model { file = "/net/cci-nas-00/data/ceres_data/8yeh_39195/06_2025/8yeh_39195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yeh_39195/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.62, per 1000 atoms: 0.38 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: 5.66 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: 2.95 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: 8.36 Time building geometry restraints manager: 6.85 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: 0.20 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: 0.790 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: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 49.950 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.370 ------------------------------------------------------------------------------- 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 : 2.356 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: 1.1643 time to fit residues: 212.0383 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 : 2.862 ------------------------------------------------------------------------------- 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 = 0.4984 r_free = 0.4984 target = 0.299825 restraints weight = 31692.032| |-----------------------------------------------------------------------------| r_work (start): 0.4969 rms_B_bonded: 1.51 r_work: 0.4873 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4873 ------------------------------------------------------------------------------- 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 : 2.409 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: 0.2966 (t-100) REVERT: F 191 ILE cc_start: 0.3671 (OUTLIER) cc_final: 0.3441 (mt) REVERT: F 388 MET cc_start: 0.0371 (mmp) cc_final: -0.1631 (tmt) REVERT: F 394 MET cc_start: 0.0443 (ttp) cc_final: 0.0240 (ttp) REVERT: L 314 GLN cc_start: -0.0452 (pt0) cc_final: -0.0980 (pt0) REVERT: L 394 MET cc_start: 0.2531 (ptm) cc_final: 0.0205 (ttp) REVERT: M 200 MET cc_start: -0.0253 (mmm) cc_final: -0.1593 (tpt) REVERT: M 299 MET cc_start: 0.2200 (mtm) cc_final: 0.1221 (ptm) REVERT: J 4 MET cc_start: -0.1538 (mtp) cc_final: -0.1882 (mtt) REVERT: N 35 TYR cc_start: 0.3868 (m-80) cc_final: 0.3285 (m-80) REVERT: N 299 MET cc_start: 0.3450 (tmm) cc_final: 0.2956 (ttt) REVERT: G 81 MET cc_start: 0.1696 (tpt) cc_final: 0.0392 (tpt) REVERT: G 108 LEU cc_start: 0.1885 (OUTLIER) cc_final: 0.0216 (tp) REVERT: O 74 ARG cc_start: 0.4537 (ttt180) cc_final: 0.3617 (ttt-90) REVERT: O 299 MET cc_start: 0.1417 (mtp) cc_final: 0.0824 (mpt) outliers start: 41 outliers final: 22 residues processed: 153 average time/residue: 1.3361 time to fit residues: 245.6203 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 : 2.934 ------------------------------------------------------------------------------- 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: 0.6980 chunk 1 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 304 optimal weight: 0.0970 chunk 149 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 overall best weight: 1.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 305 GLN F 308 ASN F 317 GLN F 320 ASN ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 153 GLN D 6 GLN ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** O 319 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5134 r_free = 0.5134 target = 0.319251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.305014 restraints weight = 31349.448| |-----------------------------------------------------------------------------| r_work (start): 0.5022 rms_B_bonded: 1.53 r_work: 0.4927 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work (final): 0.4927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1188 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25825 Z= 0.129 Angle : 0.572 13.101 35090 Z= 0.295 Chirality : 0.045 0.175 3835 Planarity : 0.005 0.066 4530 Dihedral : 4.694 23.357 3495 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.65 % Allowed : 9.39 % Favored : 88.96 % 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: 0.05 (0.36), residues: 170 sheet: -0.12 (0.16), residues: 1140 loop : -0.81 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 106 HIS 0.008 0.001 HIS O 76 PHE 0.016 0.002 PHE N 73 TYR 0.021 0.002 TYR N 242 ARG 0.005 0.001 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 370) hydrogen bonds : angle 5.35869 ( 945) SS BOND : bond 0.00306 ( 10) SS BOND : angle 0.84473 ( 20) covalent geometry : bond 0.00289 (25815) covalent geometry : angle 0.57190 (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 157 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 189 GLU cc_start: 0.2051 (OUTLIER) cc_final: 0.1246 (tt0) REVERT: F 191 ILE cc_start: 0.3655 (mt) cc_final: 0.3299 (mp) REVERT: F 328 GLN cc_start: 0.4868 (mm-40) cc_final: 0.3683 (tt0) REVERT: F 388 MET cc_start: 0.1276 (mmp) cc_final: -0.1188 (tmt) REVERT: L 314 GLN cc_start: -0.0197 (pt0) cc_final: -0.0460 (pt0) REVERT: L 330 PHE cc_start: 0.1265 (m-80) cc_final: 0.0968 (m-80) REVERT: D 1 GLN cc_start: 0.0217 (OUTLIER) cc_final: -0.0737 (tm-30) REVERT: M 200 MET cc_start: -0.0488 (mmm) cc_final: -0.1251 (tpt) REVERT: J 4 MET cc_start: -0.1062 (mtp) cc_final: -0.1286 (mtp) REVERT: N 35 TYR cc_start: 0.3517 (m-80) cc_final: 0.2912 (m-80) REVERT: N 394 MET cc_start: -0.0333 (OUTLIER) cc_final: -0.1212 (ptt) REVERT: G 81 MET cc_start: 0.2299 (tpt) cc_final: 0.1445 (tpt) REVERT: K 4 MET cc_start: 0.2387 (pmm) cc_final: 0.2078 (pmm) REVERT: O 74 ARG cc_start: 0.5340 (ttt180) cc_final: 0.4406 (ttt-90) outliers start: 46 outliers final: 21 residues processed: 139 average time/residue: 1.4108 time to fit residues: 234.7339 Evaluate side-chains 131 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 151 TYR 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 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 E residue 78 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 39 THR Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 331 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 264 optimal weight: 30.0000 chunk 158 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 257 optimal weight: 0.6980 chunk 209 optimal weight: 0.5980 chunk 300 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 319 HIS F 320 ASN ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 GLN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 314 GLN D 62 GLN I 34 ASN I 55 GLN I 89 GLN ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 ASN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 341 ASN E 30 ASN J 6 GLN ** N 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 HIS N 192 ASN ** N 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 GLN N 377 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 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5187 r_free = 0.5187 target = 0.326754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.314506 restraints weight = 32130.570| |-----------------------------------------------------------------------------| r_work (start): 0.5095 rms_B_bonded: 1.39 r_work: 0.5028 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4950 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1860 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.137 25825 Z= 0.274 Angle : 0.915 14.244 35090 Z= 0.476 Chirality : 0.056 0.287 3835 Planarity : 0.008 0.116 4530 Dihedral : 6.490 31.832 3495 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.88 % Allowed : 11.62 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.60 (0.14), residues: 3185 helix: -0.37 (0.37), residues: 170 sheet: -0.64 (0.16), residues: 1030 loop : -1.39 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 47 HIS 0.018 0.003 HIS O 120 PHE 0.054 0.004 PHE F 292 TYR 0.034 0.004 TYR M 390 ARG 0.014 0.001 ARG I 95 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 370) hydrogen bonds : angle 6.68063 ( 945) SS BOND : bond 0.00612 ( 10) SS BOND : angle 1.22708 ( 20) covalent geometry : bond 0.00588 (25815) covalent geometry : angle 0.91480 (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 237 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 129 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.1641 (m-10) cc_final: 0.0336 (m-10) REVERT: B 95 ARG cc_start: 0.5633 (ttm170) cc_final: 0.4924 (mtt90) REVERT: F 151 TYR cc_start: 0.1697 (OUTLIER) cc_final: 0.0014 (m-10) REVERT: F 189 GLU cc_start: 0.3236 (OUTLIER) cc_final: -0.0092 (tt0) REVERT: F 202 ASP cc_start: 0.2909 (OUTLIER) cc_final: 0.1994 (t70) REVERT: F 237 MET cc_start: 0.0380 (ttp) cc_final: 0.0131 (ttp) REVERT: F 328 GLN cc_start: 0.4831 (mm-40) cc_final: 0.4239 (tt0) REVERT: F 342 MET cc_start: 0.5061 (mpt) cc_final: 0.4363 (mpt) REVERT: F 388 MET cc_start: 0.1706 (mmp) cc_final: -0.1249 (tmt) REVERT: H 87 TYR cc_start: 0.3582 (m-80) cc_final: 0.3230 (m-80) REVERT: H 94 THR cc_start: 0.1102 (OUTLIER) cc_final: -0.1204 (t) REVERT: L 117 ILE cc_start: -0.1279 (OUTLIER) cc_final: -0.1886 (mp) REVERT: L 251 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6168 (mtp180) REVERT: L 277 ILE cc_start: 0.0812 (OUTLIER) cc_final: 0.0392 (mt) REVERT: L 314 GLN cc_start: 0.0300 (pt0) cc_final: -0.1324 (mt0) REVERT: L 394 MET cc_start: 0.1794 (ptt) cc_final: 0.0477 (ttp) REVERT: I 28 MET cc_start: 0.3734 (OUTLIER) cc_final: 0.3245 (mpm) REVERT: I 36 TYR cc_start: 0.2260 (m-80) cc_final: 0.0737 (m-80) REVERT: M 70 TYR cc_start: 0.1859 (m-80) cc_final: 0.1598 (m-80) REVERT: M 200 MET cc_start: -0.0160 (mmm) cc_final: -0.1352 (mmm) REVERT: M 471 GLN cc_start: 0.4338 (OUTLIER) cc_final: 0.1113 (mm-40) REVERT: J 4 MET cc_start: -0.0691 (mtp) cc_final: -0.0979 (mtt) REVERT: J 83 PHE cc_start: 0.0528 (OUTLIER) cc_final: 0.0212 (p90) REVERT: N 30 ARG cc_start: 0.1855 (mtt180) cc_final: -0.0133 (ptp90) REVERT: N 253 GLU cc_start: 0.2385 (OUTLIER) cc_final: 0.1401 (mt-10) REVERT: N 454 LYS cc_start: 0.3332 (tmtt) cc_final: 0.2819 (mppt) REVERT: G 81 MET cc_start: 0.2407 (tpt) cc_final: 0.0521 (ppp) REVERT: G 108 LEU cc_start: 0.2104 (OUTLIER) cc_final: 0.0768 (tp) REVERT: O 49 TYR cc_start: 0.3677 (OUTLIER) cc_final: 0.2675 (m-10) REVERT: O 74 ARG cc_start: 0.6377 (ttt180) cc_final: 0.5289 (ttt90) REVERT: O 355 TYR cc_start: 0.2668 (t80) cc_final: 0.0765 (t80) REVERT: O 452 LYS cc_start: 0.2855 (mttm) cc_final: 0.2576 (tptm) outliers start: 108 outliers final: 53 residues processed: 210 average time/residue: 1.0666 time to fit residues: 270.4934 Evaluate side-chains 183 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 117 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain F residue 24 THR 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 271 VAL Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 334 VAL 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 251 ARG Chi-restraints excluded: chain L residue 277 ILE Chi-restraints excluded: chain L residue 296 SER Chi-restraints excluded: chain L residue 299 MET Chi-restraints excluded: chain L residue 311 TYR Chi-restraints excluded: chain L residue 344 LEU 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 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 251 ARG Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 358 THR 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 31 ASN 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 129 THR Chi-restraints excluded: chain N residue 223 ASP 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 306 ILE Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 382 THR 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 39 THR Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 62 VAL 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 358 THR Chi-restraints excluded: chain O residue 364 LEU Chi-restraints excluded: chain O residue 373 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 115 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 258 optimal weight: 0.9990 chunk 225 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 179 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN L 153 GLN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN N 254 GLN N 377 GLN ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 GLN O 373 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5201 r_free = 0.5201 target = 0.328173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.316576 restraints weight = 31813.975| |-----------------------------------------------------------------------------| r_work (start): 0.5100 rms_B_bonded: 1.28 r_work: 0.5035 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4962 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1747 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25825 Z= 0.134 Angle : 0.621 11.450 35090 Z= 0.321 Chirality : 0.047 0.210 3835 Planarity : 0.005 0.061 4530 Dihedral : 5.358 25.772 3495 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.30 % Allowed : 14.57 % Favored : 83.13 % 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: -1.40 (0.14), residues: 3185 helix: 0.03 (0.38), residues: 170 sheet: -0.48 (0.16), residues: 1030 loop : -1.29 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 106 HIS 0.008 0.002 HIS O 120 PHE 0.019 0.002 PHE J 83 TYR 0.019 0.002 TYR N 91 ARG 0.008 0.001 ARG N 71 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 370) hydrogen bonds : angle 6.01337 ( 945) SS BOND : bond 0.00321 ( 10) SS BOND : angle 1.18654 ( 20) covalent geometry : bond 0.00301 (25815) covalent geometry : angle 0.62088 (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 191 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 127 time to evaluate : 2.482 Fit side-chains REVERT: A 64 PHE cc_start: 0.1339 (m-10) cc_final: 0.0654 (m-10) REVERT: B 95 ARG cc_start: 0.5411 (ttm170) cc_final: 0.4543 (mtp180) REVERT: F 149 MET cc_start: -0.0027 (pmm) cc_final: -0.1102 (tpt) REVERT: F 169 TRP cc_start: 0.3327 (m100) cc_final: 0.2865 (m100) REVERT: F 189 GLU cc_start: 0.2956 (OUTLIER) cc_final: 0.0000 (tp30) REVERT: F 237 MET cc_start: 0.0756 (OUTLIER) cc_final: 0.0371 (ttp) REVERT: F 292 PHE cc_start: 0.1984 (p90) cc_final: 0.1055 (p90) REVERT: F 328 GLN cc_start: 0.4646 (mm-40) cc_final: 0.3970 (tt0) REVERT: F 342 MET cc_start: 0.5130 (mpt) cc_final: 0.4301 (mpt) REVERT: F 388 MET cc_start: 0.1872 (mmp) cc_final: -0.1176 (tmt) REVERT: C 63 ARG cc_start: 0.4079 (ptt-90) cc_final: 0.3826 (ptt180) REVERT: H 87 TYR cc_start: 0.3041 (m-80) cc_final: 0.2696 (m-80) REVERT: H 94 THR cc_start: 0.0716 (OUTLIER) cc_final: -0.1387 (t) REVERT: L 159 ILE cc_start: 0.6009 (mt) cc_final: 0.5380 (pt) REVERT: L 251 ARG cc_start: 0.6837 (mtm110) cc_final: 0.6443 (mtp180) REVERT: L 252 ARG cc_start: 0.7611 (ptm160) cc_final: 0.6997 (ptp-110) REVERT: L 314 GLN cc_start: 0.0208 (OUTLIER) cc_final: -0.0477 (pt0) REVERT: L 394 MET cc_start: 0.2380 (ptt) cc_final: 0.0439 (ttp) REVERT: L 455 PHE cc_start: -0.0390 (OUTLIER) cc_final: -0.0924 (m-80) REVERT: D 69 THR cc_start: 0.1547 (OUTLIER) cc_final: 0.1098 (m) REVERT: D 81 MET cc_start: 0.2074 (ppp) cc_final: 0.1121 (pp-130) REVERT: I 36 TYR cc_start: 0.2019 (m-80) cc_final: 0.0864 (m-80) REVERT: M 200 MET cc_start: -0.0230 (mmm) cc_final: -0.1461 (mmm) REVERT: M 251 ARG cc_start: 0.1170 (OUTLIER) cc_final: -0.0063 (ttm-80) REVERT: J 83 PHE cc_start: 0.0415 (OUTLIER) cc_final: 0.0147 (p90) REVERT: N 96 GLN cc_start: 0.4897 (mm110) cc_final: 0.4423 (mt0) REVERT: N 394 MET cc_start: -0.2374 (OUTLIER) cc_final: -0.3358 (mtp) REVERT: N 454 LYS cc_start: 0.2764 (tmtt) cc_final: 0.2419 (mppt) REVERT: G 81 MET cc_start: 0.2707 (tpt) cc_final: 0.2238 (tpt) REVERT: O 74 ARG cc_start: 0.6360 (ttt180) cc_final: 0.5059 (mmm-85) REVERT: O 342 MET cc_start: -0.0100 (mtm) cc_final: -0.0614 (pp-130) outliers start: 64 outliers final: 35 residues processed: 171 average time/residue: 1.1972 time to fit residues: 245.5717 Evaluate side-chains 169 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain F residue 45 VAL 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 208 MET Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 332 THR 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 D residue 69 THR Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 336 THR 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 224 ILE Chi-restraints excluded: chain N residue 237 MET Chi-restraints excluded: chain N residue 288 SER 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 O residue 39 THR 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 327 ASN Chi-restraints excluded: chain O residue 331 VAL Chi-restraints excluded: chain O residue 455 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 287 optimal weight: 0.9990 chunk 311 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 284 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 125 optimal weight: 0.0270 chunk 310 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 0.0470 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 373 GLN C 6 GLN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN ** O 120 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 = 0.5208 r_free = 0.5208 target = 0.328868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.316992 restraints weight = 31664.192| |-----------------------------------------------------------------------------| r_work (start): 0.5103 rms_B_bonded: 1.31 r_work: 0.5038 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4964 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1638 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25825 Z= 0.093 Angle : 0.528 13.784 35090 Z= 0.269 Chirality : 0.044 0.181 3835 Planarity : 0.004 0.056 4530 Dihedral : 4.583 20.971 3495 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.12 % Allowed : 15.43 % Favored : 82.45 % 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: -1.15 (0.15), residues: 3185 helix: 0.34 (0.38), residues: 170 sheet: -0.41 (0.16), residues: 1070 loop : -1.08 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 47 HIS 0.004 0.001 HIS N 47 PHE 0.026 0.001 PHE M 261 TYR 0.015 0.001 TYR N 91 ARG 0.010 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 370) hydrogen bonds : angle 5.48730 ( 945) SS BOND : bond 0.00326 ( 10) SS BOND : angle 1.02800 ( 20) covalent geometry : bond 0.00207 (25815) covalent geometry : angle 0.52735 (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: 59 poor density : 126 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.5482 (OUTLIER) cc_final: 0.4475 (mtp180) REVERT: F 149 MET cc_start: 0.0093 (pmm) cc_final: -0.0854 (tmt) REVERT: F 237 MET cc_start: 0.0384 (OUTLIER) cc_final: 0.0093 (ttp) REVERT: F 277 ILE cc_start: 0.1223 (OUTLIER) cc_final: 0.1016 (mm) REVERT: F 292 PHE cc_start: 0.1997 (p90) cc_final: 0.1084 (p90) REVERT: F 342 MET cc_start: 0.5096 (mpt) cc_final: 0.4257 (mpt) REVERT: F 388 MET cc_start: 0.1175 (mmp) cc_final: -0.1661 (tmt) REVERT: C 63 ARG cc_start: 0.4000 (ptt-90) cc_final: 0.3027 (ptt90) REVERT: H 87 TYR cc_start: 0.2835 (m-80) cc_final: 0.2550 (m-80) REVERT: L 299 MET cc_start: 0.4611 (OUTLIER) cc_final: 0.3928 (tpt) REVERT: L 314 GLN cc_start: 0.0011 (OUTLIER) cc_final: -0.0627 (pt0) REVERT: L 330 PHE cc_start: 0.2862 (m-80) cc_final: 0.1706 (m-80) REVERT: L 394 MET cc_start: 0.2612 (ptt) cc_final: 0.0568 (ttp) REVERT: L 455 PHE cc_start: -0.0229 (OUTLIER) cc_final: -0.0754 (m-80) REVERT: D 1 GLN cc_start: 0.0579 (OUTLIER) cc_final: -0.0569 (tm-30) REVERT: D 81 MET cc_start: 0.1782 (ppp) cc_final: 0.1471 (pp-130) REVERT: I 28 MET cc_start: 0.3771 (OUTLIER) cc_final: 0.3171 (mpm) REVERT: I 36 TYR cc_start: 0.1994 (m-80) cc_final: 0.0785 (m-80) REVERT: M 200 MET cc_start: -0.0282 (mmm) cc_final: -0.0534 (mmm) REVERT: J 83 PHE cc_start: 0.0391 (OUTLIER) cc_final: 0.0061 (p90) REVERT: N 30 ARG cc_start: 0.1629 (mtt180) cc_final: -0.0000 (ptp90) REVERT: N 96 GLN cc_start: 0.4754 (mm110) cc_final: 0.4396 (mt0) REVERT: N 342 MET cc_start: 0.1686 (ttp) cc_final: 0.1261 (ttp) REVERT: G 81 MET cc_start: 0.2567 (tpt) cc_final: -0.0002 (ppp) REVERT: K 4 MET cc_start: 0.1559 (OUTLIER) cc_final: -0.2206 (ttm) REVERT: O 74 ARG cc_start: 0.6267 (ttt180) cc_final: 0.4929 (mmm-85) REVERT: O 342 MET cc_start: -0.0622 (mtm) cc_final: -0.0945 (ppp) outliers start: 59 outliers final: 33 residues processed: 165 average time/residue: 1.2095 time to fit residues: 238.6658 Evaluate side-chains 163 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 2.510 ------------------------------------------------------------------------------- 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 75 ILE Chi-restraints excluded: chain F residue 76 HIS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 277 ILE 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 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 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 28 MET Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 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 149 MET Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 237 MET Chi-restraints excluded: chain N residue 288 SER Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 382 THR Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 107 PHE 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 188 LEU Chi-restraints excluded: chain O residue 255 MET 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: 50.0000 chunk 92 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 176 optimal weight: 0.0870 chunk 8 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 GLN C 6 GLN H 38 HIS L 36 HIS L 111 GLN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 ASN L 359 ASN ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 ASN O 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5219 r_free = 0.5219 target = 0.331112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.320732 restraints weight = 31786.385| |-----------------------------------------------------------------------------| r_work (start): 0.5157 rms_B_bonded: 1.27 r_work: 0.5078 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4998 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.4998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2163 moved from start: 0.7197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25825 Z= 0.226 Angle : 0.852 15.373 35090 Z= 0.441 Chirality : 0.054 0.263 3835 Planarity : 0.007 0.078 4530 Dihedral : 6.319 31.339 3495 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 3.42 % Allowed : 14.89 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.84 (0.14), residues: 3185 helix: 0.03 (0.39), residues: 170 sheet: -0.77 (0.17), residues: 925 loop : -1.61 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP F 100 HIS 0.016 0.003 HIS M 259 PHE 0.033 0.003 PHE F 210 TYR 0.035 0.003 TYR J 92 ARG 0.011 0.001 ARG N 71 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 370) hydrogen bonds : angle 6.65992 ( 945) SS BOND : bond 0.00764 ( 10) SS BOND : angle 1.41684 ( 20) covalent geometry : bond 0.00500 (25815) covalent geometry : angle 0.85167 (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 232 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 137 time to evaluate : 2.724 Fit side-chains revert: symmetry clash REVERT: B 95 ARG cc_start: 0.5776 (OUTLIER) cc_final: 0.5127 (mtt90) REVERT: F 47 HIS cc_start: 0.3660 (OUTLIER) cc_final: 0.2507 (m170) REVERT: F 149 MET cc_start: 0.0253 (pmm) cc_final: -0.0792 (pmm) REVERT: F 169 TRP cc_start: 0.4162 (m100) cc_final: 0.3437 (m100) REVERT: F 237 MET cc_start: 0.1353 (OUTLIER) cc_final: 0.0783 (ttp) REVERT: F 342 MET cc_start: 0.5231 (mpt) cc_final: 0.4066 (mpt) REVERT: C 63 ARG cc_start: 0.4517 (ptt-90) cc_final: 0.3980 (ptt-90) REVERT: H 28 MET cc_start: 0.3293 (mmt) cc_final: 0.2078 (pp-130) REVERT: H 87 TYR cc_start: 0.3796 (m-80) cc_final: 0.3538 (m-80) REVERT: L 150 ASP cc_start: 0.3505 (OUTLIER) cc_final: 0.0182 (t0) REVERT: L 299 MET cc_start: 0.5559 (OUTLIER) cc_final: 0.4436 (tmm) REVERT: L 314 GLN cc_start: -0.0077 (OUTLIER) cc_final: -0.1169 (tt0) REVERT: L 471 GLN cc_start: 0.2554 (OUTLIER) cc_final: 0.1241 (tm130) REVERT: D 1 GLN cc_start: 0.0461 (OUTLIER) cc_final: -0.0777 (tm-30) REVERT: I 11 LEU cc_start: -0.2822 (OUTLIER) cc_final: -0.3067 (mp) REVERT: I 36 TYR cc_start: 0.2982 (m-80) cc_final: 0.1511 (m-80) REVERT: M 25 ASP cc_start: 0.1146 (m-30) cc_final: 0.0879 (p0) REVERT: M 151 TYR cc_start: 0.2366 (OUTLIER) cc_final: 0.2009 (m-80) REVERT: M 200 MET cc_start: -0.0050 (mmm) cc_final: -0.1370 (mmm) REVERT: E 48 MET cc_start: 0.4035 (OUTLIER) cc_final: 0.3808 (tpt) REVERT: J 83 PHE cc_start: 0.0648 (OUTLIER) cc_final: 0.0045 (p90) REVERT: N 30 ARG cc_start: 0.1754 (mtt180) cc_final: 0.0161 (ptp90) REVERT: N 129 THR cc_start: 0.3737 (OUTLIER) cc_final: 0.3059 (p) REVERT: N 253 GLU cc_start: 0.3393 (OUTLIER) cc_final: 0.2535 (mt-10) REVERT: N 292 PHE cc_start: 0.3949 (p90) cc_final: 0.3047 (p90) REVERT: N 299 MET cc_start: 0.3894 (OUTLIER) cc_final: 0.3590 (tpt) REVERT: N 394 MET cc_start: -0.2268 (ptt) cc_final: -0.3652 (mtm) REVERT: N 454 LYS cc_start: 0.5193 (ttpp) cc_final: 0.4168 (mppt) REVERT: G 81 MET cc_start: 0.3734 (tpt) cc_final: 0.0237 (ppp) REVERT: G 108 LEU cc_start: 0.1974 (OUTLIER) cc_final: 0.1177 (tp) REVERT: K 4 MET cc_start: 0.1889 (pmm) cc_final: 0.0840 (ptt) REVERT: K 28 MET cc_start: 0.3180 (mpp) cc_final: 0.2668 (mpp) REVERT: O 49 TYR cc_start: 0.3638 (OUTLIER) cc_final: 0.3019 (m-10) REVERT: O 74 ARG cc_start: 0.6844 (ttt180) cc_final: 0.5721 (ttt90) REVERT: O 109 ARG cc_start: 0.4248 (tpt170) cc_final: 0.3603 (tpt-90) REVERT: O 188 LEU cc_start: -0.0207 (OUTLIER) cc_final: -0.0734 (mp) REVERT: O 219 GLU cc_start: 0.3534 (OUTLIER) cc_final: 0.1154 (mp0) REVERT: O 342 MET cc_start: -0.0343 (mtm) cc_final: -0.0720 (pp-130) REVERT: O 355 TYR cc_start: 0.2426 (t80) cc_final: 0.0681 (t80) outliers start: 95 outliers final: 47 residues processed: 208 average time/residue: 1.1283 time to fit residues: 281.7617 Evaluate side-chains 196 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 130 time to evaluate : 2.388 ------------------------------------------------------------------------------- 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 76 HIS 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 237 MET Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 249 TYR Chi-restraints excluded: chain L residue 253 GLU 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 471 GLN Chi-restraints excluded: chain D residue 1 GLN 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 I residue 11 LEU Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 151 TYR Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 336 THR Chi-restraints excluded: chain M residue 459 LEU Chi-restraints excluded: chain E residue 48 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 71 ARG Chi-restraints excluded: chain N residue 88 THR 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 288 SER Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 306 ILE Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 342 MET Chi-restraints excluded: chain N residue 382 THR 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 39 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 299 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 153 GLN ** F 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 GLN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 319 HIS I 34 ASN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5226 r_free = 0.5226 target = 0.332057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.321983 restraints weight = 31792.946| |-----------------------------------------------------------------------------| r_work (start): 0.5151 rms_B_bonded: 1.24 r_work: 0.5088 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.5015 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.5015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2045 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25825 Z= 0.142 Angle : 0.645 16.825 35090 Z= 0.330 Chirality : 0.047 0.297 3835 Planarity : 0.005 0.056 4530 Dihedral : 5.491 26.066 3495 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.95 % Allowed : 16.37 % Favored : 80.68 % 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: -1.69 (0.15), residues: 3185 helix: 0.20 (0.39), residues: 170 sheet: -0.79 (0.17), residues: 1020 loop : -1.46 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 47 HIS 0.007 0.002 HIS N 47 PHE 0.019 0.002 PHE J 83 TYR 0.022 0.002 TYR O 49 ARG 0.009 0.001 ARG I 95 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 370) hydrogen bonds : angle 6.12891 ( 945) SS BOND : bond 0.00511 ( 10) SS BOND : angle 1.12335 ( 20) covalent geometry : bond 0.00321 (25815) covalent geometry : angle 0.64424 (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 210 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 128 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.5646 (OUTLIER) cc_final: 0.4971 (mtt90) REVERT: F 149 MET cc_start: 0.0122 (pmm) cc_final: -0.1170 (tmt) REVERT: F 151 TYR cc_start: 0.2102 (OUTLIER) cc_final: 0.0201 (m-10) REVERT: F 169 TRP cc_start: 0.3535 (m100) cc_final: 0.3040 (m100) REVERT: F 237 MET cc_start: 0.1296 (OUTLIER) cc_final: 0.0705 (ttp) REVERT: F 253 GLU cc_start: 0.5030 (OUTLIER) cc_final: 0.3783 (mt-10) REVERT: F 342 MET cc_start: 0.5482 (mpt) cc_final: 0.4471 (mpt) REVERT: C 63 ARG cc_start: 0.4349 (ptt-90) cc_final: 0.3863 (ptt180) REVERT: H 28 MET cc_start: 0.2893 (mmt) cc_final: 0.1975 (pp-130) REVERT: L 299 MET cc_start: 0.5683 (OUTLIER) cc_final: 0.4126 (tmm) REVERT: L 314 GLN cc_start: -0.0024 (OUTLIER) cc_final: -0.1290 (tt0) REVERT: L 394 MET cc_start: 0.3089 (ptt) cc_final: 0.0750 (ttp) REVERT: L 455 PHE cc_start: 0.0323 (OUTLIER) cc_final: 0.0061 (m-80) REVERT: I 28 MET cc_start: 0.4917 (OUTLIER) cc_final: 0.4375 (mpm) REVERT: I 36 TYR cc_start: 0.2950 (m-80) cc_final: 0.1512 (m-80) REVERT: M 25 ASP cc_start: 0.1265 (m-30) cc_final: 0.0925 (p0) REVERT: M 200 MET cc_start: -0.0130 (mmm) cc_final: -0.1283 (mmm) REVERT: M 248 PHE cc_start: 0.3279 (OUTLIER) cc_final: 0.0842 (p90) REVERT: M 299 MET cc_start: 0.2532 (tpp) cc_final: 0.0955 (tmm) REVERT: J 83 PHE cc_start: 0.0668 (OUTLIER) cc_final: 0.0057 (p90) REVERT: N 30 ARG cc_start: 0.1439 (mtt180) cc_final: 0.0187 (ptp90) REVERT: N 129 THR cc_start: 0.3733 (OUTLIER) cc_final: 0.2944 (p) REVERT: N 292 PHE cc_start: 0.3762 (p90) cc_final: 0.3049 (p90) REVERT: N 299 MET cc_start: 0.3771 (tpt) cc_final: 0.3415 (tpt) REVERT: N 375 ILE cc_start: 0.2174 (OUTLIER) cc_final: 0.1785 (mm) REVERT: N 455 PHE cc_start: 0.3970 (OUTLIER) cc_final: 0.2848 (m-10) REVERT: G 81 MET cc_start: 0.3425 (tpt) cc_final: 0.0189 (ppp) REVERT: G 108 LEU cc_start: 0.2016 (OUTLIER) cc_final: 0.0832 (tp) REVERT: K 4 MET cc_start: 0.1619 (pmm) cc_final: 0.0013 (ptt) REVERT: K 28 MET cc_start: 0.3055 (mpp) cc_final: 0.2373 (mpp) REVERT: O 49 TYR cc_start: 0.3219 (OUTLIER) cc_final: 0.2858 (m-10) REVERT: O 74 ARG cc_start: 0.6676 (ttt180) cc_final: 0.5377 (ttt180) REVERT: O 120 HIS cc_start: 0.4574 (OUTLIER) cc_final: 0.3250 (t-170) REVERT: O 188 LEU cc_start: -0.0018 (OUTLIER) cc_final: -0.0488 (mp) REVERT: O 342 MET cc_start: -0.0343 (mtm) cc_final: -0.0800 (ppp) outliers start: 82 outliers final: 46 residues processed: 184 average time/residue: 1.1361 time to fit residues: 253.0744 Evaluate side-chains 190 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 127 time to evaluate : 2.575 ------------------------------------------------------------------------------- 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 76 HIS 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 237 MET Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 107 VAL 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 344 LEU 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 28 MET Chi-restraints excluded: chain M residue 47 HIS Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 248 PHE Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 336 THR Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 459 LEU 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 71 ARG Chi-restraints excluded: chain N residue 88 THR 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 288 SER Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 382 THR 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 39 THR 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 255 MET Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 364 LEU 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: 10.0000 chunk 246 optimal weight: 0.5980 chunk 122 optimal weight: 0.1980 chunk 17 optimal weight: 0.0670 chunk 34 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 299 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 263 optimal weight: 7.9990 chunk 284 optimal weight: 3.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 214 GLN M 143 ASN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 216 ASN O 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5207 r_free = 0.5207 target = 0.331776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.319864 restraints weight = 32359.319| |-----------------------------------------------------------------------------| r_work (start): 0.5102 rms_B_bonded: 1.48 r_work: 0.5042 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4964 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1866 moved from start: 0.7194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 25825 Z= 0.096 Angle : 0.543 17.544 35090 Z= 0.276 Chirality : 0.045 0.283 3835 Planarity : 0.005 0.059 4530 Dihedral : 4.700 20.757 3495 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.27 % Allowed : 17.09 % Favored : 80.65 % 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: -1.37 (0.15), residues: 3185 helix: 0.60 (0.39), residues: 170 sheet: -0.56 (0.17), residues: 1050 loop : -1.27 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 106 HIS 0.004 0.001 HIS O 168 PHE 0.019 0.001 PHE J 83 TYR 0.013 0.001 TYR L 249 ARG 0.006 0.000 ARG L 251 Details of bonding type rmsd hydrogen bonds : bond 0.02789 ( 370) hydrogen bonds : angle 5.59100 ( 945) SS BOND : bond 0.00347 ( 10) SS BOND : angle 0.97777 ( 20) covalent geometry : bond 0.00214 (25815) covalent geometry : angle 0.54269 (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 190 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 127 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.5332 (OUTLIER) cc_final: 0.4658 (mtm180) REVERT: F 169 TRP cc_start: 0.3122 (m100) cc_final: 0.2812 (m100) REVERT: F 237 MET cc_start: 0.0500 (OUTLIER) cc_final: 0.0115 (ttp) REVERT: F 253 GLU cc_start: 0.4816 (OUTLIER) cc_final: 0.3786 (mt-10) REVERT: F 342 MET cc_start: 0.5301 (mpt) cc_final: 0.4349 (mpt) REVERT: C 63 ARG cc_start: 0.4464 (ptt-90) cc_final: 0.4143 (ptt180) REVERT: H 28 MET cc_start: 0.2907 (mmt) cc_final: 0.2018 (pp-130) REVERT: L 299 MET cc_start: 0.5448 (OUTLIER) cc_final: 0.4298 (tpt) REVERT: L 314 GLN cc_start: 0.0422 (OUTLIER) cc_final: 0.0080 (pt0) REVERT: L 394 MET cc_start: 0.2985 (ptt) cc_final: 0.0828 (ttp) REVERT: D 81 MET cc_start: 0.0084 (pp-130) cc_final: -0.0203 (pp-130) REVERT: I 28 MET cc_start: 0.4266 (OUTLIER) cc_final: 0.3582 (mpm) REVERT: I 36 TYR cc_start: 0.2739 (m-80) cc_final: 0.1359 (m-80) REVERT: M 200 MET cc_start: 0.0056 (mmm) cc_final: -0.0949 (ppp) REVERT: M 299 MET cc_start: 0.2009 (OUTLIER) cc_final: 0.0344 (tmm) REVERT: E 69 THR cc_start: -0.0076 (OUTLIER) cc_final: -0.0854 (t) REVERT: J 83 PHE cc_start: 0.0830 (OUTLIER) cc_final: 0.0181 (p90) REVERT: N 30 ARG cc_start: 0.1311 (mtt180) cc_final: -0.0093 (ptp90) REVERT: N 129 THR cc_start: 0.3479 (OUTLIER) cc_final: 0.2577 (p) REVERT: N 375 ILE cc_start: 0.1817 (OUTLIER) cc_final: 0.1373 (mm) REVERT: N 394 MET cc_start: -0.2709 (pp-130) cc_final: -0.3031 (tpp) REVERT: N 455 PHE cc_start: 0.4004 (OUTLIER) cc_final: 0.3021 (m-10) REVERT: G 81 MET cc_start: 0.3380 (tpt) cc_final: 0.0910 (tmm) REVERT: G 108 LEU cc_start: 0.1951 (OUTLIER) cc_final: 0.0246 (tp) REVERT: K 28 MET cc_start: 0.2837 (mpp) cc_final: 0.2190 (mpp) REVERT: O 74 ARG cc_start: 0.6499 (ttt180) cc_final: 0.4584 (mtt180) REVERT: O 188 LEU cc_start: -0.0160 (OUTLIER) cc_final: -0.0579 (mp) REVERT: O 219 GLU cc_start: 0.2873 (OUTLIER) cc_final: 0.0929 (mm-30) REVERT: O 342 MET cc_start: -0.0543 (mtm) cc_final: -0.0984 (ppp) outliers start: 63 outliers final: 37 residues processed: 172 average time/residue: 1.1667 time to fit residues: 240.4430 Evaluate side-chains 175 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 2.811 ------------------------------------------------------------------------------- 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 99 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 299 MET Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain M residue 115 VAL 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 71 ARG Chi-restraints excluded: chain N residue 88 THR 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 288 SER Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 382 THR 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 153 GLN 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 271 VAL Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 364 LEU 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: 0.0040 chunk 289 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 251 optimal weight: 0.0980 chunk 303 optimal weight: 0.0170 chunk 107 optimal weight: 0.0370 chunk 64 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 overall best weight: 0.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 96 GLN D 1 GLN ** M 216 ASN ** 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 = 0.5202 r_free = 0.5202 target = 0.331174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.319373 restraints weight = 32301.926| |-----------------------------------------------------------------------------| r_work (start): 0.5111 rms_B_bonded: 1.57 r_work: 0.5043 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4962 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1739 moved from start: 0.7089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25825 Z= 0.082 Angle : 0.503 17.353 35090 Z= 0.253 Chirality : 0.044 0.241 3835 Planarity : 0.004 0.058 4530 Dihedral : 4.161 18.782 3495 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.47 % Allowed : 17.77 % Favored : 80.76 % 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: -1.11 (0.15), residues: 3185 helix: 1.00 (0.40), residues: 170 sheet: -0.51 (0.16), residues: 1085 loop : -1.02 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 47 HIS 0.003 0.001 HIS N 120 PHE 0.018 0.001 PHE J 83 TYR 0.013 0.001 TYR K 49 ARG 0.012 0.000 ARG I 95 Details of bonding type rmsd hydrogen bonds : bond 0.02455 ( 370) hydrogen bonds : angle 5.17235 ( 945) SS BOND : bond 0.00327 ( 10) SS BOND : angle 0.93986 ( 20) covalent geometry : bond 0.00186 (25815) covalent geometry : angle 0.50293 (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 167 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 2.346 Fit side-chains revert: symmetry clash REVERT: B 95 ARG cc_start: 0.5382 (OUTLIER) cc_final: 0.4246 (mtp180) REVERT: F 149 MET cc_start: -0.0323 (pmm) cc_final: -0.1200 (ptt) REVERT: F 169 TRP cc_start: 0.3186 (m100) cc_final: 0.2885 (m100) REVERT: F 237 MET cc_start: 0.0458 (OUTLIER) cc_final: 0.0134 (ttp) REVERT: F 342 MET cc_start: 0.5304 (mpt) cc_final: 0.4392 (mpt) REVERT: F 388 MET cc_start: 0.0265 (OUTLIER) cc_final: -0.2437 (tmt) REVERT: C 63 ARG cc_start: 0.4065 (ptt-90) cc_final: 0.3232 (ptt-90) REVERT: H 28 MET cc_start: 0.2648 (mmt) cc_final: 0.1885 (pp-130) REVERT: H 94 THR cc_start: 0.0711 (OUTLIER) cc_final: -0.1385 (t) REVERT: L 225 CYS cc_start: 0.3413 (OUTLIER) cc_final: 0.3080 (m) REVERT: L 299 MET cc_start: 0.5434 (OUTLIER) cc_final: 0.4246 (tpt) REVERT: L 330 PHE cc_start: 0.4388 (m-80) cc_final: 0.3289 (m-80) REVERT: L 394 MET cc_start: 0.2587 (ptt) cc_final: 0.0622 (ttp) REVERT: D 48 MET cc_start: 0.3571 (tpp) cc_final: 0.2914 (ttt) REVERT: I 28 MET cc_start: 0.3891 (OUTLIER) cc_final: 0.3263 (mpm) REVERT: I 34 ASN cc_start: 0.6786 (m110) cc_final: 0.6310 (m-40) REVERT: I 36 TYR cc_start: 0.2726 (m-80) cc_final: 0.1387 (m-80) REVERT: M 200 MET cc_start: 0.0276 (mmm) cc_final: -0.0819 (ppp) REVERT: M 299 MET cc_start: 0.1322 (tpp) cc_final: -0.0101 (tmm) REVERT: E 69 THR cc_start: -0.0219 (OUTLIER) cc_final: -0.0913 (t) REVERT: J 83 PHE cc_start: 0.0697 (OUTLIER) cc_final: 0.0302 (p90) REVERT: N 96 GLN cc_start: 0.4464 (mm110) cc_final: 0.3937 (mt0) REVERT: N 111 GLN cc_start: 0.3268 (mm-40) cc_final: 0.1391 (pt0) REVERT: N 342 MET cc_start: 0.2163 (pmm) cc_final: 0.1160 (ptm) REVERT: N 375 ILE cc_start: 0.1779 (OUTLIER) cc_final: 0.1364 (mm) REVERT: N 394 MET cc_start: -0.2390 (pp-130) cc_final: -0.3013 (tpp) REVERT: N 455 PHE cc_start: 0.3712 (OUTLIER) cc_final: 0.2885 (m-80) REVERT: G 81 MET cc_start: 0.3419 (tpt) cc_final: 0.1056 (tmm) REVERT: K 4 MET cc_start: 0.1181 (pmm) cc_final: -0.2209 (mpp) REVERT: K 28 MET cc_start: 0.2660 (mpp) cc_final: 0.1943 (mpp) REVERT: O 74 ARG cc_start: 0.6297 (ttt180) cc_final: 0.4720 (ttt90) REVERT: O 188 LEU cc_start: -0.0075 (OUTLIER) cc_final: -0.0521 (mp) REVERT: O 342 MET cc_start: -0.0698 (mtm) cc_final: -0.1236 (ppp) outliers start: 41 outliers final: 24 residues processed: 153 average time/residue: 1.1632 time to fit residues: 212.6720 Evaluate side-chains 160 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 2.495 ------------------------------------------------------------------------------- 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 151 TYR Chi-restraints excluded: chain F residue 237 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 F residue 388 MET Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 225 CYS Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 299 MET Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain M residue 115 VAL 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 71 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 237 MET Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 382 THR 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 188 LEU Chi-restraints excluded: chain O residue 255 MET 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: 0.0370 chunk 250 optimal weight: 2.9990 chunk 173 optimal weight: 0.0040 chunk 140 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 overall best weight: 1.1874 ------------------------------------------------------------------------------- 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 D 1 GLN M 155 GLN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 216 ASN ** 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 = 0.5216 r_free = 0.5216 target = 0.332924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.321349 restraints weight = 32146.317| |-----------------------------------------------------------------------------| r_work (start): 0.5117 rms_B_bonded: 1.46 r_work: 0.5059 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4983 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.4983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1975 moved from start: 0.7534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25825 Z= 0.122 Angle : 0.586 17.007 35090 Z= 0.296 Chirality : 0.045 0.175 3835 Planarity : 0.005 0.061 4530 Dihedral : 4.679 19.936 3495 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.94 % Allowed : 17.37 % Favored : 80.68 % 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: -1.24 (0.15), residues: 3185 helix: 0.94 (0.40), residues: 170 sheet: -0.65 (0.16), residues: 1090 loop : -1.08 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 47 HIS 0.007 0.001 HIS N 120 PHE 0.026 0.002 PHE F 292 TYR 0.014 0.002 TYR M 234 ARG 0.018 0.001 ARG F 263 Details of bonding type rmsd hydrogen bonds : bond 0.02850 ( 370) hydrogen bonds : angle 5.50066 ( 945) SS BOND : bond 0.00439 ( 10) SS BOND : angle 1.02725 ( 20) covalent geometry : bond 0.00276 (25815) covalent geometry : angle 0.58518 (35070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15042.09 seconds wall clock time: 263 minutes 5.26 seconds (15785.26 seconds total)