Starting phenix.real_space_refine on Fri Sep 19 09:16:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yeh_39195/09_2025/8yeh_39195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yeh_39195/09_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_39195/09_2025/8yeh_39195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yeh_39195/09_2025/8yeh_39195.map" model { file = "/net/cci-nas-00/data/ceres_data/8yeh_39195/09_2025/8yeh_39195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yeh_39195/09_2025/8yeh_39195.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: C, D, E, G, H, I, J, K, L, M, N, O Time building chain proxies: 4.33, per 1000 atoms: 0.17 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 D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 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: 2.01 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.7 microseconds 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: 0.92 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: 4.58 Time building geometry restraints manager: 2.75 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.830 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG J 24 TYR 0.015 0.001 TYR C 32 PHE 0.031 0.002 PHE N 455 TRP 0.008 0.001 TRP G 36 HIS 0.005 0.001 HIS L 120 Details of bonding type rmsd covalent geometry : bond 0.00306 (25815) covalent geometry : angle 0.55490 (35070) SS BOND : bond 0.00585 ( 10) SS BOND : angle 1.13967 ( 20) hydrogen bonds : bond 0.14258 ( 370) hydrogen bonds : angle 5.41583 ( 945) *********************** 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 : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 191 ILE cc_start: 0.1027 (mt) cc_final: 0.0722 (mt) REVERT: C 48 MET cc_start: 0.0646 (mtp) cc_final: -0.0855 (ppp) REVERT: N 212 THR cc_start: 0.1671 (p) cc_final: 0.1317 (t) REVERT: N 214 GLN cc_start: 0.3781 (mt0) cc_final: 0.2999 (mt0) REVERT: G 117 LEU cc_start: 0.3235 (tp) cc_final: 0.2928 (pt) REVERT: O 74 ARG cc_start: 0.1935 (ttt180) cc_final: 0.1622 (ttt180) REVERT: O 151 TYR cc_start: 0.2264 (m-10) cc_final: 0.1000 (m-80) REVERT: O 342 MET cc_start: 0.2164 (mtm) cc_final: 0.1107 (pp-130) outliers start: 0 outliers final: 1 residues processed: 152 average time/residue: 0.5468 time to fit residues: 98.7757 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 : 0.758 ------------------------------------------------------------------------------- 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 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 120 HIS F 305 GLN F 314 GLN C 1 GLN H 38 HIS L 192 ASN L 285 ASN L 305 GLN I 38 HIS M 155 GLN M 285 ASN M 305 GLN M 373 GLN E 6 GLN E 30 ASN J 38 HIS N 143 ASN ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 377 GLN G 30 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 192 ASN O 328 GLN O 359 ASN O 373 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.312768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.293851 restraints weight = 31810.001| |-----------------------------------------------------------------------------| r_work (start): 0.4927 rms_B_bonded: 1.74 r_work: 0.4855 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.4855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0909 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 25825 Z= 0.203 Angle : 0.747 14.159 35090 Z= 0.387 Chirality : 0.051 0.245 3835 Planarity : 0.007 0.080 4530 Dihedral : 5.118 81.367 3498 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.12 % Allowed : 6.65 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.14), residues: 3185 helix: -0.06 (0.35), residues: 175 sheet: 0.15 (0.16), residues: 1145 loop : -0.70 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 100 TYR 0.035 0.003 TYR L 291 PHE 0.036 0.003 PHE M 374 TRP 0.020 0.002 TRP A 36 HIS 0.015 0.002 HIS M 120 Details of bonding type rmsd covalent geometry : bond 0.00453 (25815) covalent geometry : angle 0.74663 (35070) SS BOND : bond 0.00491 ( 10) SS BOND : angle 1.54214 ( 20) hydrogen bonds : bond 0.04019 ( 370) hydrogen bonds : angle 5.63310 ( 945) *********************** 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 161 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.3617 (t-100) cc_final: 0.2935 (t-100) REVERT: F 191 ILE cc_start: 0.3323 (mt) cc_final: 0.3007 (mt) REVERT: F 328 GLN cc_start: 0.4746 (mm-40) cc_final: 0.3874 (tt0) REVERT: F 388 MET cc_start: 0.0976 (mmp) cc_final: -0.1316 (tmt) REVERT: C 1 GLN cc_start: -0.0242 (OUTLIER) cc_final: -0.1324 (tp40) REVERT: L 388 MET cc_start: -0.0284 (mmm) cc_final: -0.0532 (mmp) REVERT: L 394 MET cc_start: 0.2652 (ptm) cc_final: 0.0381 (ttp) REVERT: I 34 ASN cc_start: 0.5646 (OUTLIER) cc_final: 0.4660 (p0) REVERT: M 200 MET cc_start: -0.0520 (mmm) cc_final: -0.1784 (tmt) REVERT: M 394 MET cc_start: -0.2979 (ttt) cc_final: -0.3612 (ppp) REVERT: J 4 MET cc_start: -0.1219 (mtp) cc_final: -0.1613 (mtt) REVERT: N 35 TYR cc_start: 0.3686 (m-80) cc_final: 0.2968 (m-80) REVERT: N 299 MET cc_start: 0.3081 (tmm) cc_final: 0.2655 (ttt) REVERT: G 81 MET cc_start: 0.1719 (tpt) cc_final: 0.0388 (tpt) REVERT: O 74 ARG cc_start: 0.4186 (ttt180) cc_final: 0.3197 (ttt90) REVERT: O 342 MET cc_start: 0.0067 (mtm) cc_final: -0.0475 (pp-130) outliers start: 31 outliers final: 13 residues processed: 143 average time/residue: 0.5277 time to fit residues: 91.0539 Evaluate side-chains 129 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 332 THR 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 34 THR Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain O residue 193 THR 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 240 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 257 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 270 optimal weight: 8.9990 chunk 314 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 38 HIS F 76 HIS F 143 ASN F 153 GLN F 192 ASN F 285 ASN ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN F 319 HIS F 320 ASN L 153 GLN L 314 GLN D 1 GLN D 6 GLN D 62 GLN ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 ASN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 341 ASN J 6 GLN ** N 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 GLN ** N 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 GLN N 359 ASN ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 ASN O 153 GLN O 216 ASN ** O 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 ASN O 305 GLN ** O 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 373 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.321651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.307408 restraints weight = 32167.482| |-----------------------------------------------------------------------------| r_work (start): 0.5024 rms_B_bonded: 1.71 r_work: 0.4949 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4866 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1573 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.197 25825 Z= 0.242 Angle : 0.839 12.437 35090 Z= 0.439 Chirality : 0.053 0.227 3835 Planarity : 0.007 0.079 4530 Dihedral : 5.963 30.429 3495 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.84 % Allowed : 10.14 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.14), residues: 3185 helix: -0.16 (0.37), residues: 170 sheet: -0.35 (0.16), residues: 1030 loop : -1.16 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 71 TYR 0.053 0.003 TYR N 242 PHE 0.032 0.003 PHE A 64 TRP 0.031 0.003 TRP E 106 HIS 0.021 0.003 HIS O 120 Details of bonding type rmsd covalent geometry : bond 0.00545 (25815) covalent geometry : angle 0.83902 (35070) SS BOND : bond 0.00592 ( 10) SS BOND : angle 1.23765 ( 20) hydrogen bonds : bond 0.04850 ( 370) hydrogen bonds : angle 6.04579 ( 945) *********************** 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 204 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 125 time to evaluate : 0.950 Fit side-chains REVERT: B 95 ARG cc_start: 0.5503 (ttm170) cc_final: 0.4573 (mtp180) REVERT: F 151 TYR cc_start: 0.1604 (OUTLIER) cc_final: -0.0251 (m-10) REVERT: F 189 GLU cc_start: 0.2671 (OUTLIER) cc_final: 0.1407 (tt0) REVERT: F 328 GLN cc_start: 0.4975 (mm-40) cc_final: 0.4200 (tt0) REVERT: F 388 MET cc_start: 0.1395 (mmp) cc_final: -0.1446 (tmt) REVERT: C 1 GLN cc_start: -0.1213 (OUTLIER) cc_final: -0.2830 (tt0) REVERT: H 94 THR cc_start: 0.0776 (OUTLIER) cc_final: -0.1336 (t) REVERT: L 277 ILE cc_start: 0.0756 (OUTLIER) cc_final: 0.0366 (mt) REVERT: L 314 GLN cc_start: 0.0048 (pt0) cc_final: -0.0458 (pt0) REVERT: I 36 TYR cc_start: 0.1492 (m-80) cc_final: 0.0353 (m-80) REVERT: M 70 TYR cc_start: 0.1906 (m-80) cc_final: 0.1524 (m-80) REVERT: M 200 MET cc_start: -0.0304 (mmm) cc_final: -0.1637 (tpt) REVERT: M 251 ARG cc_start: 0.1185 (OUTLIER) cc_final: -0.0314 (ttt180) REVERT: N 35 TYR cc_start: 0.4538 (m-80) cc_final: 0.4170 (m-80) REVERT: N 129 THR cc_start: 0.3958 (OUTLIER) cc_final: 0.2609 (m) REVERT: G 81 MET cc_start: 0.3117 (tpt) cc_final: 0.2692 (tpt) REVERT: G 108 LEU cc_start: 0.2102 (OUTLIER) cc_final: 0.0045 (tp) REVERT: O 74 ARG cc_start: 0.6075 (ttt180) cc_final: 0.4925 (ttt-90) REVERT: O 355 TYR cc_start: 0.2451 (t80) cc_final: 0.0778 (t80) outliers start: 79 outliers final: 35 residues processed: 181 average time/residue: 0.5239 time to fit residues: 113.0536 Evaluate side-chains 161 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain C residue 1 GLN 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 296 SER Chi-restraints excluded: chain L residue 364 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 149 MET Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 336 THR Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain N residue 47 HIS 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 313 LEU Chi-restraints excluded: chain N residue 333 VAL 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 108 LEU Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 120 HIS Chi-restraints excluded: chain O residue 319 HIS Chi-restraints excluded: chain O residue 327 ASN Chi-restraints excluded: chain O residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 61 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 206 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 303 optimal weight: 0.1980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 314 GLN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 1 GLN L 153 GLN I 90 GLN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 341 ASN E 39 GLN N 254 GLN O 96 GLN ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 319 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5165 r_free = 0.5165 target = 0.323930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.310707 restraints weight = 31782.161| |-----------------------------------------------------------------------------| r_work (start): 0.5056 rms_B_bonded: 1.35 r_work: 0.4982 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4904 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1384 moved from start: 0.4695 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= 0.101 Angle : 0.536 10.227 35090 Z= 0.276 Chirality : 0.045 0.171 3835 Planarity : 0.005 0.064 4530 Dihedral : 4.662 24.628 3495 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.69 % Allowed : 12.09 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.15), residues: 3185 helix: 0.26 (0.38), residues: 170 sheet: -0.24 (0.16), residues: 1065 loop : -0.88 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 95 TYR 0.020 0.001 TYR N 91 PHE 0.021 0.001 PHE J 83 TRP 0.019 0.001 TRP D 47 HIS 0.010 0.001 HIS O 120 Details of bonding type rmsd covalent geometry : bond 0.00223 (25815) covalent geometry : angle 0.53579 (35070) SS BOND : bond 0.00229 ( 10) SS BOND : angle 0.69413 ( 20) hydrogen bonds : bond 0.02891 ( 370) hydrogen bonds : angle 5.46701 ( 945) *********************** 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 162 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 64 PHE cc_start: 0.1063 (m-10) cc_final: 0.0555 (m-10) REVERT: A 90 ASP cc_start: -0.0315 (OUTLIER) cc_final: -0.0720 (t70) REVERT: B 95 ARG cc_start: 0.5341 (ttm170) cc_final: 0.4160 (mtp180) REVERT: F 202 ASP cc_start: 0.2922 (OUTLIER) cc_final: 0.2291 (t70) REVERT: F 328 GLN cc_start: 0.4664 (mm-40) cc_final: 0.4002 (tt0) REVERT: F 388 MET cc_start: 0.1429 (mmp) cc_final: -0.1535 (tmt) REVERT: C 1 GLN cc_start: -0.1236 (OUTLIER) cc_final: -0.2018 (tp-100) REVERT: L 251 ARG cc_start: 0.8201 (ptp-110) cc_final: 0.6733 (ptt90) REVERT: L 314 GLN cc_start: 0.0069 (pt0) cc_final: -0.0363 (pt0) REVERT: D 1 GLN cc_start: 0.0379 (OUTLIER) cc_final: -0.0554 (tm-30) REVERT: D 101 LEU cc_start: 0.1635 (OUTLIER) cc_final: 0.0465 (tp) REVERT: I 28 MET cc_start: 0.3216 (OUTLIER) cc_final: 0.2675 (mpm) REVERT: M 200 MET cc_start: -0.0581 (mmm) cc_final: -0.1103 (mmm) REVERT: N 35 TYR cc_start: 0.3584 (m-80) cc_final: 0.3087 (m-80) REVERT: N 394 MET cc_start: -0.0822 (ttt) cc_final: -0.3004 (ptt) REVERT: G 81 MET cc_start: 0.2523 (tpt) cc_final: 0.1937 (tpt) REVERT: O 74 ARG cc_start: 0.5822 (ttt180) cc_final: 0.4428 (ttt90) REVERT: O 152 LYS cc_start: 0.2970 (OUTLIER) cc_final: 0.2667 (tmtt) outliers start: 47 outliers final: 24 residues processed: 147 average time/residue: 0.5913 time to fit residues: 103.0933 Evaluate side-chains 142 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain M residue 149 MET Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain N residue 47 HIS Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 237 MET Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 382 THR Chi-restraints excluded: chain N residue 455 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 152 LYS Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain O residue 299 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 6 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 303 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 113 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN F 96 GLN ** L 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN I 34 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** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 341 ASN E 30 ASN N 155 GLN N 192 ASN N 327 ASN O 96 GLN ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5155 r_free = 0.5155 target = 0.325728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.5119 r_free = 0.5119 target = 0.320998 restraints weight = 30158.594| |-----------------------------------------------------------------------------| r_work (start): 0.5140 rms_B_bonded: 0.47 r_work: 0.5074 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.4983 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2036 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25825 Z= 0.230 Angle : 0.840 13.513 35090 Z= 0.436 Chirality : 0.053 0.235 3835 Planarity : 0.007 0.107 4530 Dihedral : 6.174 29.646 3495 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.63 % Allowed : 13.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.14), residues: 3185 helix: -0.07 (0.38), residues: 160 sheet: -0.77 (0.16), residues: 1045 loop : -1.35 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 109 TYR 0.029 0.003 TYR J 36 PHE 0.033 0.004 PHE L 248 TRP 0.034 0.003 TRP F 100 HIS 0.014 0.003 HIS O 120 Details of bonding type rmsd covalent geometry : bond 0.00515 (25815) covalent geometry : angle 0.83994 (35070) SS BOND : bond 0.00547 ( 10) SS BOND : angle 1.20530 ( 20) hydrogen bonds : bond 0.04204 ( 370) hydrogen bonds : angle 6.53554 ( 945) *********************** 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 236 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 135 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.1584 (m-10) cc_final: 0.0516 (m-10) REVERT: B 95 ARG cc_start: 0.5752 (ttm170) cc_final: 0.4901 (mtt90) REVERT: F 45 VAL cc_start: 0.1247 (OUTLIER) cc_final: 0.0991 (m) REVERT: F 151 TYR cc_start: 0.2051 (OUTLIER) cc_final: 0.0258 (m-10) REVERT: F 189 GLU cc_start: 0.3409 (OUTLIER) cc_final: 0.2056 (tm-30) REVERT: F 202 ASP cc_start: 0.3031 (OUTLIER) cc_final: 0.2829 (m-30) REVERT: F 313 LEU cc_start: 0.3585 (OUTLIER) cc_final: 0.2980 (pp) REVERT: F 342 MET cc_start: 0.5362 (mpt) cc_final: 0.4423 (mpt) REVERT: C 63 ARG cc_start: 0.4005 (ptt-90) cc_final: 0.3352 (ptt90) REVERT: H 87 TYR cc_start: 0.3573 (m-80) cc_final: 0.3183 (m-80) REVERT: H 94 THR cc_start: 0.0937 (OUTLIER) cc_final: -0.1278 (t) REVERT: L 117 ILE cc_start: -0.1202 (OUTLIER) cc_final: -0.1468 (mt) REVERT: L 150 ASP cc_start: 0.3490 (OUTLIER) cc_final: 0.0314 (t0) REVERT: L 299 MET cc_start: 0.3230 (OUTLIER) cc_final: 0.0359 (ptt) REVERT: L 314 GLN cc_start: 0.0482 (OUTLIER) cc_final: -0.1053 (tt0) REVERT: L 363 TYR cc_start: 0.2765 (OUTLIER) cc_final: 0.2479 (m-80) REVERT: D 1 GLN cc_start: 0.0493 (OUTLIER) cc_final: -0.0642 (tm-30) REVERT: D 101 LEU cc_start: 0.2548 (OUTLIER) cc_final: 0.1810 (mt) REVERT: I 28 MET cc_start: 0.4869 (OUTLIER) cc_final: 0.4212 (mpm) REVERT: I 36 TYR cc_start: 0.2292 (m-80) cc_final: 0.1058 (m-80) REVERT: M 149 MET cc_start: 0.2141 (OUTLIER) cc_final: 0.1921 (mtp) REVERT: M 151 TYR cc_start: 0.2484 (OUTLIER) cc_final: 0.1998 (m-80) REVERT: M 200 MET cc_start: -0.0142 (mmm) cc_final: -0.1345 (mmm) REVERT: M 471 GLN cc_start: 0.4782 (OUTLIER) cc_final: 0.1671 (mp10) REVERT: J 83 PHE cc_start: 0.0936 (OUTLIER) cc_final: 0.0241 (p90) REVERT: N 30 ARG cc_start: 0.1970 (mtt180) cc_final: 0.0306 (ptp90) REVERT: N 253 GLU cc_start: 0.2581 (OUTLIER) cc_final: 0.1613 (mt-10) REVERT: G 81 MET cc_start: 0.2858 (tpt) cc_final: 0.0729 (ppp) REVERT: G 108 LEU cc_start: 0.2416 (OUTLIER) cc_final: 0.0443 (tp) REVERT: K 4 MET cc_start: 0.2799 (OUTLIER) cc_final: 0.0983 (ptt) REVERT: O 74 ARG cc_start: 0.6415 (ttt180) cc_final: 0.5540 (ttt90) REVERT: O 152 LYS cc_start: 0.3273 (OUTLIER) cc_final: 0.2610 (tmtm) REVERT: O 262 ASN cc_start: 0.4634 (m110) cc_final: 0.4402 (t0) REVERT: O 342 MET cc_start: 0.0149 (mtm) cc_final: -0.0376 (pp-130) REVERT: O 355 TYR cc_start: 0.2532 (t80) cc_final: 0.0776 (t80) outliers start: 101 outliers final: 51 residues processed: 215 average time/residue: 0.5222 time to fit residues: 134.6086 Evaluate side-chains 198 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 125 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain F residue 24 THR 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 151 TYR Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain H residue 34 ASN 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 225 CYS 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 363 TYR Chi-restraints excluded: chain L residue 364 LEU 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 D residue 101 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 149 MET Chi-restraints excluded: chain M residue 151 TYR Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 471 GLN 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 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 N residue 388 MET 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 51 ILE Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 152 LYS Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain O residue 327 ASN Chi-restraints excluded: chain O residue 358 THR 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 263 optimal weight: 1.9990 chunk 150 optimal weight: 0.0970 chunk 21 optimal weight: 0.2980 chunk 239 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 191 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 GLN ** I 90 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** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 377 GLN G 30 ASN ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5208 r_free = 0.5208 target = 0.329611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5117 r_free = 0.5117 target = 0.318250 restraints weight = 31837.211| |-----------------------------------------------------------------------------| r_work (start): 0.5125 rms_B_bonded: 1.28 r_work: 0.5049 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4970 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1693 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25825 Z= 0.098 Angle : 0.550 11.020 35090 Z= 0.283 Chirality : 0.045 0.172 3835 Planarity : 0.005 0.057 4530 Dihedral : 4.815 23.566 3495 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.16 % Allowed : 15.54 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.15), residues: 3185 helix: 0.12 (0.38), residues: 170 sheet: -0.49 (0.16), residues: 1070 loop : -1.12 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 252 TYR 0.017 0.001 TYR N 91 PHE 0.027 0.002 PHE L 248 TRP 0.026 0.001 TRP D 47 HIS 0.005 0.001 HIS O 120 Details of bonding type rmsd covalent geometry : bond 0.00217 (25815) covalent geometry : angle 0.54988 (35070) SS BOND : bond 0.00258 ( 10) SS BOND : angle 0.69388 ( 20) hydrogen bonds : bond 0.02912 ( 370) hydrogen bonds : angle 5.65604 ( 945) *********************** 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 183 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 123 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.1394 (m-10) cc_final: 0.1007 (m-10) REVERT: B 95 ARG cc_start: 0.5378 (ttm170) cc_final: 0.4357 (mtp180) REVERT: F 47 HIS cc_start: 0.3090 (OUTLIER) cc_final: 0.2214 (m170) REVERT: F 149 MET cc_start: -0.0603 (pmm) cc_final: -0.1046 (tmt) REVERT: F 169 TRP cc_start: 0.3068 (m100) cc_final: 0.2772 (m100) REVERT: F 342 MET cc_start: 0.5063 (mpt) cc_final: 0.4396 (mpt) REVERT: H 87 TYR cc_start: 0.2958 (m-80) cc_final: 0.2640 (m-80) REVERT: L 299 MET cc_start: 0.2825 (tpp) cc_final: 0.0105 (pmm) REVERT: L 314 GLN cc_start: 0.0122 (OUTLIER) cc_final: -0.0428 (pt0) REVERT: L 363 TYR cc_start: 0.2779 (OUTLIER) cc_final: 0.2485 (m-80) REVERT: L 394 MET cc_start: 0.3029 (ptt) cc_final: 0.0935 (ttp) REVERT: L 455 PHE cc_start: -0.0025 (OUTLIER) cc_final: -0.0559 (m-80) REVERT: D 81 MET cc_start: 0.1530 (ppp) cc_final: 0.0669 (pp-130) REVERT: D 101 LEU cc_start: 0.2278 (OUTLIER) cc_final: 0.1191 (tp) REVERT: I 28 MET cc_start: 0.4240 (mmt) cc_final: 0.3565 (mpm) REVERT: I 36 TYR cc_start: 0.2160 (m-80) cc_final: 0.0914 (m-80) REVERT: M 200 MET cc_start: -0.0256 (mmm) cc_final: -0.1496 (mmm) REVERT: M 394 MET cc_start: -0.1916 (mtt) cc_final: -0.3658 (ptt) REVERT: J 83 PHE cc_start: 0.0543 (OUTLIER) cc_final: 0.0048 (p90) REVERT: N 96 GLN cc_start: 0.4885 (mm110) cc_final: 0.4384 (mt0) REVERT: N 111 GLN cc_start: 0.2917 (mm-40) cc_final: 0.1062 (pt0) REVERT: N 342 MET cc_start: 0.1571 (OUTLIER) cc_final: 0.0680 (ttp) REVERT: N 394 MET cc_start: -0.0565 (ttt) cc_final: -0.3011 (ptt) REVERT: G 81 MET cc_start: 0.2930 (tpt) cc_final: 0.2539 (tpt) REVERT: K 4 MET cc_start: 0.1628 (OUTLIER) cc_final: 0.0001 (ptt) REVERT: K 28 MET cc_start: 0.3576 (mtp) cc_final: 0.3086 (mpp) REVERT: O 74 ARG cc_start: 0.6123 (ttt180) cc_final: 0.4936 (mmm-85) REVERT: O 342 MET cc_start: -0.0611 (mtm) cc_final: -0.0868 (ppp) outliers start: 60 outliers final: 32 residues processed: 169 average time/residue: 0.5470 time to fit residues: 110.5462 Evaluate side-chains 161 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 365 ARG Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain L residue 363 TYR Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain M residue 358 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 237 MET Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 342 MET Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 455 PHE 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 152 LYS Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 260 LEU 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 269 optimal weight: 2.9990 chunk 265 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 234 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 254 optimal weight: 2.9990 chunk 271 optimal weight: 9.9990 chunk 112 optimal weight: 0.0670 chunk 183 optimal weight: 3.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 111 GLN L 36 HIS ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5212 r_free = 0.5212 target = 0.330180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.319311 restraints weight = 31799.432| |-----------------------------------------------------------------------------| r_work (start): 0.5136 rms_B_bonded: 1.29 r_work: 0.5064 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4985 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1927 moved from start: 0.6719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25825 Z= 0.149 Angle : 0.637 10.321 35090 Z= 0.327 Chirality : 0.047 0.176 3835 Planarity : 0.005 0.056 4530 Dihedral : 5.162 22.938 3495 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.06 % Allowed : 15.36 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.15), residues: 3185 helix: 0.22 (0.39), residues: 170 sheet: -0.65 (0.17), residues: 1025 loop : -1.23 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 109 TYR 0.019 0.002 TYR J 92 PHE 0.027 0.002 PHE L 248 TRP 0.022 0.002 TRP F 100 HIS 0.010 0.002 HIS O 120 Details of bonding type rmsd covalent geometry : bond 0.00334 (25815) covalent geometry : angle 0.63728 (35070) SS BOND : bond 0.00376 ( 10) SS BOND : angle 0.73240 ( 20) hydrogen bonds : bond 0.03154 ( 370) hydrogen bonds : angle 5.86542 ( 945) *********************** 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 211 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 126 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.1450 (m-10) cc_final: 0.0681 (m-10) REVERT: B 95 ARG cc_start: 0.5718 (OUTLIER) cc_final: 0.4721 (mtt90) REVERT: F 47 HIS cc_start: 0.3275 (OUTLIER) cc_final: 0.2469 (m170) REVERT: F 149 MET cc_start: -0.0261 (pmm) cc_final: -0.1153 (tmt) REVERT: F 169 TRP cc_start: 0.3720 (m100) cc_final: 0.3115 (m100) REVERT: F 237 MET cc_start: 0.0889 (OUTLIER) cc_final: 0.0342 (ttp) REVERT: F 342 MET cc_start: 0.5375 (mpt) cc_final: 0.4418 (mpt) REVERT: C 48 MET cc_start: 0.3192 (mtp) cc_final: 0.0499 (ptm) REVERT: C 63 ARG cc_start: 0.4158 (ptt180) cc_final: 0.2953 (ptt-90) REVERT: H 94 THR cc_start: 0.0888 (OUTLIER) cc_final: -0.1380 (t) REVERT: L 299 MET cc_start: 0.3474 (tpp) cc_final: 0.0696 (pmm) REVERT: L 314 GLN cc_start: 0.0122 (OUTLIER) cc_final: -0.0565 (pt0) REVERT: L 363 TYR cc_start: 0.2897 (OUTLIER) cc_final: 0.2573 (m-80) REVERT: L 394 MET cc_start: 0.3291 (ptt) cc_final: 0.0975 (ttp) REVERT: L 455 PHE cc_start: 0.0305 (OUTLIER) cc_final: -0.0583 (m-80) REVERT: L 471 GLN cc_start: 0.2138 (OUTLIER) cc_final: 0.1006 (tm130) REVERT: D 81 MET cc_start: 0.1433 (ppp) cc_final: 0.0642 (pp-130) REVERT: D 101 LEU cc_start: 0.2170 (OUTLIER) cc_final: 0.1757 (mt) REVERT: I 11 LEU cc_start: -0.2405 (OUTLIER) cc_final: -0.2757 (mp) REVERT: I 28 MET cc_start: 0.4784 (OUTLIER) cc_final: 0.4124 (mpm) REVERT: I 36 TYR cc_start: 0.2555 (m-80) cc_final: 0.1219 (m-80) REVERT: M 200 MET cc_start: -0.0173 (mmm) cc_final: -0.1317 (mmm) REVERT: M 251 ARG cc_start: 0.0868 (OUTLIER) cc_final: -0.0445 (ttt-90) REVERT: J 83 PHE cc_start: 0.0505 (OUTLIER) cc_final: -0.0029 (p90) REVERT: N 30 ARG cc_start: 0.1382 (mtt180) cc_final: -0.0208 (ptp90) REVERT: N 253 GLU cc_start: 0.2969 (OUTLIER) cc_final: 0.2097 (mt-10) REVERT: G 81 MET cc_start: 0.3340 (tpt) cc_final: 0.0079 (ppp) REVERT: K 4 MET cc_start: 0.1730 (OUTLIER) cc_final: 0.0258 (ptt) REVERT: O 74 ARG cc_start: 0.6494 (ttt180) cc_final: 0.5427 (ttt90) REVERT: O 120 HIS cc_start: 0.4584 (OUTLIER) cc_final: 0.3088 (t-170) REVERT: O 152 LYS cc_start: 0.3093 (OUTLIER) cc_final: 0.2838 (tmmm) outliers start: 85 outliers final: 50 residues processed: 187 average time/residue: 0.5658 time to fit residues: 126.2308 Evaluate side-chains 192 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 125 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 365 ARG Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 363 TYR Chi-restraints excluded: chain L residue 364 LEU Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 471 GLN Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 459 LEU 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 237 MET Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 288 SER 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 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 108 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 120 HIS Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 152 LYS Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain O residue 319 HIS Chi-restraints excluded: chain O residue 327 ASN Chi-restraints excluded: chain O residue 364 LEU Chi-restraints excluded: chain O residue 455 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 259 optimal weight: 0.3980 chunk 241 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 168 HIS ** F 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN L 290 ASN I 6 GLN ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 254 GLN M 290 ASN ** M 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 319 HIS N 377 GLN ** O 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.335106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5170 r_free = 0.5170 target = 0.325448 restraints weight = 31945.204| |-----------------------------------------------------------------------------| r_work (start): 0.5164 rms_B_bonded: 1.23 r_work: 0.5097 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.5019 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.5019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2332 moved from start: 0.8071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 25825 Z= 0.253 Angle : 0.901 12.260 35090 Z= 0.468 Chirality : 0.056 0.274 3835 Planarity : 0.007 0.109 4530 Dihedral : 6.664 29.699 3495 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.67 % Allowed : 15.54 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.14), residues: 3185 helix: -0.40 (0.37), residues: 173 sheet: -1.09 (0.17), residues: 1011 loop : -1.71 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 71 TYR 0.029 0.004 TYR J 92 PHE 0.043 0.004 PHE K 98 TRP 0.041 0.003 TRP F 100 HIS 0.030 0.003 HIS O 120 Details of bonding type rmsd covalent geometry : bond 0.00564 (25815) covalent geometry : angle 0.90015 (35070) SS BOND : bond 0.00709 ( 10) SS BOND : angle 1.52786 ( 20) hydrogen bonds : bond 0.04392 ( 370) hydrogen bonds : angle 7.13202 ( 945) *********************** 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 245 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 143 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.1910 (m-10) cc_final: 0.0894 (m-10) REVERT: B 95 ARG cc_start: 0.5842 (OUTLIER) cc_final: 0.5067 (mtt90) REVERT: F 47 HIS cc_start: 0.4038 (OUTLIER) cc_final: 0.2746 (m170) REVERT: F 76 HIS cc_start: 0.4855 (m90) cc_final: 0.4544 (m170) REVERT: F 149 MET cc_start: -0.0211 (pmm) cc_final: -0.1037 (pmm) REVERT: F 151 TYR cc_start: 0.2131 (OUTLIER) cc_final: -0.0056 (m-10) REVERT: F 237 MET cc_start: 0.1465 (OUTLIER) cc_final: 0.0862 (ttp) REVERT: F 253 GLU cc_start: 0.5100 (OUTLIER) cc_final: 0.3860 (pt0) REVERT: F 342 MET cc_start: 0.5481 (mpt) cc_final: 0.4325 (mpt) REVERT: C 47 TRP cc_start: 0.2164 (t-100) cc_final: 0.0711 (t-100) REVERT: C 63 ARG cc_start: 0.4314 (ptt180) cc_final: 0.2932 (mtp180) REVERT: H 28 MET cc_start: 0.3106 (mmt) cc_final: 0.1534 (pp-130) REVERT: H 87 TYR cc_start: 0.4262 (m-80) cc_final: 0.4024 (m-80) REVERT: L 299 MET cc_start: 0.4372 (tpp) cc_final: 0.4001 (tpt) REVERT: L 314 GLN cc_start: 0.0096 (OUTLIER) cc_final: -0.1030 (tt0) REVERT: L 363 TYR cc_start: 0.2932 (OUTLIER) cc_final: 0.2513 (m-80) REVERT: D 52 VAL cc_start: 0.2016 (OUTLIER) cc_final: 0.1757 (t) REVERT: D 69 THR cc_start: 0.2163 (OUTLIER) cc_final: 0.1651 (m) REVERT: I 11 LEU cc_start: -0.2197 (OUTLIER) cc_final: -0.2593 (mp) REVERT: I 28 MET cc_start: 0.5171 (OUTLIER) cc_final: 0.4542 (mpm) REVERT: I 36 TYR cc_start: 0.3294 (m-80) cc_final: 0.1809 (m-80) REVERT: M 200 MET cc_start: 0.0422 (mmm) cc_final: -0.0543 (ppp) REVERT: M 251 ARG cc_start: 0.1544 (OUTLIER) cc_final: -0.0354 (ttt-90) REVERT: E 36 TRP cc_start: 0.4805 (m100) cc_final: 0.2739 (m100) REVERT: J 83 PHE cc_start: 0.0710 (OUTLIER) cc_final: 0.0312 (p90) REVERT: N 30 ARG cc_start: 0.1635 (mtt180) cc_final: 0.1036 (pmt-80) REVERT: N 208 MET cc_start: 0.4419 (ptt) cc_final: 0.3964 (ptt) REVERT: N 253 GLU cc_start: 0.3557 (OUTLIER) cc_final: 0.2582 (mt-10) REVERT: N 342 MET cc_start: 0.2243 (ttp) cc_final: 0.1439 (ptt) REVERT: N 375 ILE cc_start: 0.2732 (OUTLIER) cc_final: 0.2354 (mm) REVERT: N 455 PHE cc_start: 0.4257 (OUTLIER) cc_final: 0.2661 (m-10) REVERT: G 81 MET cc_start: 0.4115 (tpt) cc_final: 0.1907 (tmm) REVERT: G 107 PHE cc_start: 0.3736 (OUTLIER) cc_final: 0.3254 (p90) REVERT: G 108 LEU cc_start: 0.1872 (OUTLIER) cc_final: 0.1256 (tp) REVERT: K 4 MET cc_start: 0.1467 (OUTLIER) cc_final: 0.0510 (ptt) REVERT: O 120 HIS cc_start: 0.3888 (OUTLIER) cc_final: 0.2697 (m170) REVERT: O 188 LEU cc_start: 0.0446 (OUTLIER) cc_final: -0.0579 (mp) REVERT: O 219 GLU cc_start: 0.3107 (OUTLIER) cc_final: 0.1140 (mp0) REVERT: O 342 MET cc_start: -0.0021 (mtm) cc_final: -0.0380 (pp-130) outliers start: 102 outliers final: 50 residues processed: 224 average time/residue: 0.5259 time to fit residues: 141.8861 Evaluate side-chains 210 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 138 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain B residue 90 GLN 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 69 GLN Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 253 GLU 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 335 ASP Chi-restraints excluded: chain F residue 365 ARG Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 249 TYR Chi-restraints excluded: chain L residue 311 TYR Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain L residue 363 TYR Chi-restraints excluded: chain L residue 364 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 459 LEU 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 147 ILE Chi-restraints excluded: chain N residue 220 VAL Chi-restraints excluded: chain N residue 253 GLU 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 54 ILE Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 120 HIS Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 152 LYS Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 219 GLU Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 299 MET Chi-restraints excluded: chain O residue 319 HIS Chi-restraints excluded: chain O residue 327 ASN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 345 CYS Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain O residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 303 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 231 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 290 ASN C 1 GLN D 1 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5245 r_free = 0.5245 target = 0.334938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5164 r_free = 0.5164 target = 0.325072 restraints weight = 31794.263| |-----------------------------------------------------------------------------| r_work (start): 0.5180 rms_B_bonded: 1.26 r_work: 0.5110 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.5030 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.5030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2220 moved from start: 0.8147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25825 Z= 0.168 Angle : 0.695 12.225 35090 Z= 0.359 Chirality : 0.049 0.431 3835 Planarity : 0.006 0.066 4530 Dihedral : 5.906 24.437 3495 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.55 % Allowed : 16.91 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.14), residues: 3185 helix: -0.44 (0.36), residues: 177 sheet: -1.05 (0.17), residues: 988 loop : -1.64 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 71 TYR 0.019 0.002 TYR J 36 PHE 0.025 0.002 PHE K 98 TRP 0.038 0.002 TRP D 47 HIS 0.008 0.002 HIS N 47 Details of bonding type rmsd covalent geometry : bond 0.00377 (25815) covalent geometry : angle 0.69500 (35070) SS BOND : bond 0.00491 ( 10) SS BOND : angle 0.89671 ( 20) hydrogen bonds : bond 0.03532 ( 370) hydrogen bonds : angle 6.58759 ( 945) *********************** 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 212 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 141 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.2179 (m-10) cc_final: 0.1252 (m-10) REVERT: B 95 ARG cc_start: 0.5837 (OUTLIER) cc_final: 0.4926 (mtt90) REVERT: F 47 HIS cc_start: 0.3872 (OUTLIER) cc_final: 0.2539 (m170) REVERT: F 76 HIS cc_start: 0.4770 (m90) cc_final: 0.4403 (m170) REVERT: F 151 TYR cc_start: 0.1952 (OUTLIER) cc_final: -0.0026 (m-10) REVERT: F 169 TRP cc_start: 0.3793 (m100) cc_final: 0.3250 (m100) REVERT: F 237 MET cc_start: 0.1276 (OUTLIER) cc_final: 0.0593 (ttp) REVERT: F 253 GLU cc_start: 0.5120 (OUTLIER) cc_final: 0.3894 (mt-10) REVERT: F 342 MET cc_start: 0.5389 (mpt) cc_final: 0.4289 (mpt) REVERT: C 36 TRP cc_start: 0.2250 (m-90) cc_final: 0.2042 (m-90) REVERT: C 63 ARG cc_start: 0.4585 (ptt180) cc_final: 0.3043 (mtp180) REVERT: H 28 MET cc_start: 0.2850 (mmt) cc_final: 0.2123 (pp-130) REVERT: H 87 TYR cc_start: 0.4028 (m-80) cc_final: 0.3814 (m-80) REVERT: L 314 GLN cc_start: 0.0033 (OUTLIER) cc_final: -0.1438 (tt0) REVERT: D 1 GLN cc_start: 0.1541 (OUTLIER) cc_final: 0.1296 (tp40) REVERT: D 81 MET cc_start: 0.1905 (ppp) cc_final: 0.1056 (pp-130) REVERT: I 11 LEU cc_start: -0.2162 (OUTLIER) cc_final: -0.2452 (mp) REVERT: I 28 MET cc_start: 0.5011 (OUTLIER) cc_final: 0.4379 (mpm) REVERT: I 36 TYR cc_start: 0.3144 (m-80) cc_final: 0.1698 (m-80) REVERT: M 237 MET cc_start: 0.1246 (ttp) cc_final: 0.0991 (ttp) REVERT: M 251 ARG cc_start: 0.1154 (OUTLIER) cc_final: -0.0195 (ttt-90) REVERT: M 394 MET cc_start: -0.1834 (mtt) cc_final: -0.3654 (ptt) REVERT: E 36 TRP cc_start: 0.4681 (m100) cc_final: 0.2573 (m100) REVERT: J 83 PHE cc_start: 0.0814 (OUTLIER) cc_final: 0.0376 (p90) REVERT: N 149 MET cc_start: 0.2897 (ptp) cc_final: 0.2664 (ptp) REVERT: N 253 GLU cc_start: 0.3472 (OUTLIER) cc_final: 0.2689 (mt-10) REVERT: N 375 ILE cc_start: 0.2755 (OUTLIER) cc_final: 0.2366 (mm) REVERT: N 455 PHE cc_start: 0.4209 (OUTLIER) cc_final: 0.2602 (m-80) REVERT: G 108 LEU cc_start: 0.2184 (OUTLIER) cc_final: -0.0092 (pt) REVERT: K 4 MET cc_start: 0.1690 (OUTLIER) cc_final: 0.0244 (ptt) REVERT: O 49 TYR cc_start: 0.3439 (OUTLIER) cc_final: 0.3044 (m-10) REVERT: O 188 LEU cc_start: 0.0841 (OUTLIER) cc_final: 0.0607 (mt) REVERT: O 342 MET cc_start: -0.0240 (mtm) cc_final: -0.0609 (pp-130) outliers start: 71 outliers final: 46 residues processed: 195 average time/residue: 0.5497 time to fit residues: 128.4788 Evaluate side-chains 198 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 134 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 253 GLU 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 335 ASP Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 311 TYR Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain L residue 364 LEU Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain M residue 47 HIS Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 251 ARG Chi-restraints excluded: chain M residue 459 LEU 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 115 VAL Chi-restraints excluded: chain N residue 220 VAL Chi-restraints excluded: chain N residue 253 GLU 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 K residue 4 MET Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 152 LYS Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain O residue 319 HIS Chi-restraints excluded: chain O residue 327 ASN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain O residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 71 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 309 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 201 optimal weight: 20.0000 chunk 131 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 chunk 228 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 168 HIS F 373 GLN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 143 ASN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 377 GLN O 120 HIS O 305 GLN O 450 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.335495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5166 r_free = 0.5166 target = 0.325306 restraints weight = 31891.880| |-----------------------------------------------------------------------------| r_work (start): 0.5181 rms_B_bonded: 1.30 r_work: 0.5111 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.5031 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.5031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2049 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25825 Z= 0.107 Angle : 0.585 13.008 35090 Z= 0.299 Chirality : 0.046 0.271 3835 Planarity : 0.005 0.057 4530 Dihedral : 5.159 24.752 3495 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.76 % Allowed : 17.77 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.15), residues: 3185 helix: 0.04 (0.39), residues: 171 sheet: -0.90 (0.17), residues: 1011 loop : -1.49 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 252 TYR 0.016 0.001 TYR L 249 PHE 0.019 0.002 PHE J 83 TRP 0.057 0.002 TRP D 47 HIS 0.005 0.001 HIS O 120 Details of bonding type rmsd covalent geometry : bond 0.00239 (25815) covalent geometry : angle 0.58482 (35070) SS BOND : bond 0.00322 ( 10) SS BOND : angle 0.82595 ( 20) hydrogen bonds : bond 0.02947 ( 370) hydrogen bonds : angle 6.00713 ( 945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.5698 (OUTLIER) cc_final: 0.4899 (mtt90) REVERT: F 47 HIS cc_start: 0.3992 (OUTLIER) cc_final: 0.2636 (m170) REVERT: F 76 HIS cc_start: 0.4594 (m90) cc_final: 0.4311 (m170) REVERT: F 169 TRP cc_start: 0.3362 (m100) cc_final: 0.2976 (m100) REVERT: F 237 MET cc_start: 0.0883 (OUTLIER) cc_final: -0.0029 (ttp) REVERT: F 342 MET cc_start: 0.5096 (mpt) cc_final: 0.4056 (mpt) REVERT: C 48 MET cc_start: 0.3831 (mtp) cc_final: 0.2691 (ptm) REVERT: C 63 ARG cc_start: 0.4583 (ptt180) cc_final: 0.3082 (mtp180) REVERT: H 28 MET cc_start: 0.2923 (mmt) cc_final: 0.2206 (pp-130) REVERT: L 314 GLN cc_start: 0.0054 (OUTLIER) cc_final: -0.0165 (pt0) REVERT: D 81 MET cc_start: 0.2032 (ppp) cc_final: 0.1606 (pp-130) REVERT: I 28 MET cc_start: 0.4899 (OUTLIER) cc_final: 0.4275 (mpm) REVERT: I 36 TYR cc_start: 0.3018 (m-80) cc_final: 0.1543 (m-80) REVERT: E 36 TRP cc_start: 0.4500 (m100) cc_final: 0.2479 (m100) REVERT: E 48 MET cc_start: 0.2437 (ppp) cc_final: 0.1975 (tmt) REVERT: E 81 MET cc_start: -0.0403 (OUTLIER) cc_final: -0.1195 (tmm) REVERT: J 83 PHE cc_start: 0.0669 (OUTLIER) cc_final: 0.0355 (p90) REVERT: N 111 GLN cc_start: 0.2837 (mm-40) cc_final: 0.1193 (pt0) REVERT: N 342 MET cc_start: 0.1735 (ttp) cc_final: 0.0307 (ttp) REVERT: N 375 ILE cc_start: 0.2468 (OUTLIER) cc_final: 0.2029 (mm) REVERT: N 455 PHE cc_start: 0.4206 (OUTLIER) cc_final: 0.2776 (m-80) REVERT: G 81 MET cc_start: 0.4057 (OUTLIER) cc_final: -0.0607 (ppp) REVERT: G 108 LEU cc_start: 0.2106 (OUTLIER) cc_final: -0.0005 (pt) REVERT: K 4 MET cc_start: 0.1417 (OUTLIER) cc_final: -0.0130 (ptt) REVERT: O 120 HIS cc_start: 0.4209 (OUTLIER) cc_final: 0.2894 (t-170) REVERT: O 342 MET cc_start: -0.0271 (mtm) cc_final: -0.0808 (pp-130) outliers start: 49 outliers final: 25 residues processed: 165 average time/residue: 0.5306 time to fit residues: 105.3314 Evaluate side-chains 166 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 314 GLN Chi-restraints excluded: chain L residue 364 LEU Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain M residue 47 HIS 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 220 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 37 VAL Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 120 HIS Chi-restraints excluded: chain O residue 152 LYS Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain O residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 50 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 164 optimal weight: 0.0670 chunk 293 optimal weight: 1.9990 chunk 154 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 192 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 153 GLN L 155 GLN D 1 GLN ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 GLN ** M 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5257 r_free = 0.5257 target = 0.336486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5176 r_free = 0.5176 target = 0.326626 restraints weight = 31874.714| |-----------------------------------------------------------------------------| r_work (start): 0.5191 rms_B_bonded: 1.26 r_work: 0.5119 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.5040 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.5040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2076 moved from start: 0.8137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25825 Z= 0.111 Angle : 0.588 13.199 35090 Z= 0.299 Chirality : 0.046 0.204 3835 Planarity : 0.005 0.059 4530 Dihedral : 5.016 21.130 3495 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.98 % Allowed : 17.70 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.15), residues: 3185 helix: 0.12 (0.39), residues: 171 sheet: -0.89 (0.17), residues: 1036 loop : -1.43 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 252 TYR 0.014 0.001 TYR L 249 PHE 0.023 0.002 PHE J 83 TRP 0.069 0.002 TRP D 47 HIS 0.010 0.001 HIS O 120 Details of bonding type rmsd covalent geometry : bond 0.00248 (25815) covalent geometry : angle 0.58730 (35070) SS BOND : bond 0.00371 ( 10) SS BOND : angle 0.86550 ( 20) hydrogen bonds : bond 0.03042 ( 370) hydrogen bonds : angle 5.91461 ( 945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7226.88 seconds wall clock time: 124 minutes 27.20 seconds (7467.20 seconds total)